Wouldn't the atheist movement be immediately discredited if God miraculously proved his existence once and for all to everybody? If He put the 10 commandments on the Moon, nobody could argue otherwise. The Bible gives cryptic clues, but nothing clear. Paul talks about Creation being evidence for a Creator. Modern evolutionary theory disputes that.
In addition, many of Jesus' miracles are disputed as debatable and subjective: blindness can sometimes occur and leave; cripples could be subjectively healed or even planted! There are even modern, naturalistic, cases where a dead person came back to life (literally after being in a morgue) for several weeks. "Why doesn't God heal amputees?" where the limb has to indisputably be miraculously regrown.
Skepticism over 'Violations of Nature'
The bias against the supernatural isn't that new. Already Spinoza (1632-1677) denied the existence of miracles because they "violated natural law." In a lecture in the early 1900's, Adolf von Harnack stated that in ancient times the laws of nature weren't well understood or respected, and as a result we encounter countless miracle stories. Miracles can't exist because they break the immutable nature of reality.
Harnack might be correct about the origin of many miracle stories, but certainly not about his unconditional adherence to the laws of nature. He spoke around 1909, a time when Einstein's General of Theory of Relativity hadn't even been published (1916) or tested (1919), shaking the world by the rejection of Newtonian physics. It's a characteristic mark of the 19th century, carried over from the physical accomplishments since the days of the Enlightenment, to blindly believe in their progress' inerrant superiority and to question all tradition. Not only was the Bible considered full of forgery, but also the authenticity of various ancient texts, such as Herodotus' Histories, or Tacitus' Annals. Euripides' genius in Tragedy was even eclipsed [Arthur S. Day ed., Euripides Vol. I (Loeb Classical Library: 1916, pp.ix-x)]. The general attitude that prevailed was one of being close to answering all questions about the universe: there was literally a (rather short) list of questions left unanswered until the theory of "everything" was complete.
This carried over into mathematics. In the early 20th century, the great mathematician, David Hilbert, inaugurated a famous quest to have all results in math reduced to a complete set of consistent axioms. This attempt was frustrated by Kurt Gödel in 1931 when his Incompleteness Theorems proved this was impossible. The result was expanded beyond mathematics and more philosophically for logic in 1936 by Alfred Tarski with his Undefinability Theorem, and that same year Alan Turing did the same for Computer Science and the Halting Problem. With so many negative results, it almost seems like math, science, and logic were crashing down, especially compared with the previous century's confidence and optimism. If only skeptics of religion would see that errors in the conclusions of a philosopher do not necessarily imply mistakes in the philosophy: not only were many ingenious men mistaken in math and science, but it almost seemed like the subjects themselves had holes.
At any rate, the point is that Harnack lived at a time when these facts about the erroneous nature of his and others' dogmatic view of reality and the universe were still in the future. Even if we take a naturalistic view, we know from Quantum Mechanics that classical physics breaks down at the subatomic level, and in places such as at the singularity of a black hole. And the laws of nature weren't always the way they are now - they were formed and stabilized some time in the finite past after the Big Bang.
Father Andrew Pinsent, research director of the Ian Ramsey Centre for Science and Religion at Oxford University, states that "a scientific perspective does not rule out miracles," and that laws merely describe objects without the intervention of personal agents:
if I throw an apple in the air, its trajectory will approximate a parabola that can be predicted from its initial position and momentum, but that prediction says nothing about whether or not I choose to catch the apple. And if I can intervene to change the trajectory of an apple then presumably God, who is all-powerful, can do the same and much more. [Fatima at 100: Can a scientist take Fatima seriously?, Catholic Herald, May 11, 2017]
Lack of empirical, verifiable, reliable Evidence
I won't argue miracles happened. Instead, the idea behind them and someone's validity. Of course, the perception of a miracle always astounded, both in ancient times and now, and carried authority (Mark 3:22-26, John 2:18, 23, 3:2, 10:25, 32). With the rise of modern science, we have far fewer claims of supernatural activity. But the numerous reports of UFOs and ghosts show that man will always be interested in mysteries.
Some legitimate wonders can actually be obscured by modern science. For example, mathematical prodigies who can calculate large numbers were (verifiably!) far more numerous in earlier times than now, with the rise of calculators and other machines. Noting prodigies from the past such as Zerah Colburn and Zacharias Dase, Ogilvy and Anderson write:
Nearly all of the older books about numbers or mathematical recreations contain accounts of calculating prodigies. The arithmetical wizard was a subject of wonder and admiration to the nineteenth- and early twentieth-century reader. Today there seems to be less general interest in the human calculator, perhaps because his feats have been so far surpassed by his mechanical counterpart. When a Colburn or a Dase multiplied two large numbers together in one-twentieth of the time it would take to do the arithmetic by longhand, people were impressed partly because there was no other way to get the answer. But now, when a machine can do the same "problem" in a twenty-thousandth of the time, with virtually no chance of error, the human performance, while just as noteworthy as it always was, fails to make the same impression. It happens that there have been no famous calculating boys born in the twentieth century. When the next one turns up, it is a safe bet that his appearance will cause little stir. [Excursions in Number Theory (1981), pp.106-7]
So it's not because mathematical prodigies were "invented" in the 19th and early 20th (and earlier) centuries - they simply faded out in the face of technology. The opposite case exists in modern times: artists and sculptors of Leonardo Da Vinci's and Michelangelo's calibre existed long before (e.g. Phidias); but nowadays thanks to modern rules (and machines!), one can become comparable with just a little bit of talent. These men and their abilities weren't invented in ancient times.
So why should we also assume miracles never existed? Superstitions were quickly disregarded by educated men (Council of Paderborn in 785 considers witches a superstition). Pliny the Younger actually anticipates gravity due to his belief in a round Earth, saying that perhaps there is some force that "allows men's feet to face each other" while standing on the other side of the world! Josephus regards earthquakes as purely natural, occuring once in a while but frequently in Judea to cause a lot of death and destruction.
Sure there were always hustlers that people believed, but direct, widely-known, genuinely verifiable wonders were also considered rare in ancient times (Judges 6:12-13 - none for centuries since Egypt). Few miracle workers in the Talmud, such as Hanina ben Dosa (yet see the Jewish predilection towards the supernatural - 1 Cor. 1:22). Even the Messiah in Jewish thought wasn't considered a miracle worker. When Jesus heals a blind man, he responds, "Never since the world began has it been heard that anyone opened the eyes of a man born blind" (John 9:32). This obvious exaggeration is why a public occurrence is not always enough for credibility: it needs reliable reporting. This is why John 4:54 calls the healing of the official's son, which would've been quite notable and pointless for the official to fabricate, the second sign, despite having done many signs between this and the first (John 2:23).
This goes to show how poor records were as we mentioned, and even then they were merely what we might regard as "old wives' tales" today (whether accurately or not is another question). Most of the communication with God was through prophets or the Urim and Thummim: nothing direct. Similarly, the priests themselves didn't often hear from God directly: in 1 Samuel 3:1 it's stated that visions from God were rare in those days, because of sins (Judges 2:1).
There are a handful of miracles in the entire Bible that were seen by enough people to maybe be recorded, especially with ancient illiteracy rates (Exodus, Joshua's Long Day, Resurrection). The famous cliche, "absence of evidence isn't evidence of absence," could be invoked. After all, that's what atheists do when claiming they don't have to prove a negative.
"Why doesn't God heal amputees?" Restored sight could be natural or psychosomatic (e.g. the temporary blindness of Richard Burton's companion, John Speke, on one of their trips in Africa). The same could be said of many illnesses. But a restored limb is something else. Maybe the severed ear Jesus puts back (Luke 22:50-51) and a king's hand that withers and is restored (1 Kings 13:4-6) count and the healings of the paralyzed and lame/crippled come close (Mark 2:1-12; John 5:1-17). As was said, miracles were always very rare. But I'm sure that there must've been many people missing legs/arms/fingers/eyes, but there were far more sick, hungry, and crippled/dead people whose story made it.
The Great Deception
But why does God "hide"? Not only does he remain invisible by the Bible's own admission (Col. 1:15, 1 Tim. 1:17, Heb. 11:27), but Paul explicitly states in 2 Thess. 2:9-12 that God purposely confuses the damned:
The coming of the lawless one is based on Satan’s working, with all kinds of false miracles, signs, and wonders, and with every unrighteous deception among those who are perishing. They perish because they did not accept the love of the truth in order to be saved. For this reason God sends them a strong delusion so that they will believe what is false, so that all will be condemned—those who did not believe the truth but enjoyed unrighteousness. (HCSB)
Well how does this square with God's invitation for all to be saved (Matthew 22:8-9, 2 Pet. 3:9)?
The outcome God wants is different from the reality. While He wants to save everyone, He knows not only will that not happen, most won't (Matt. 7:13). In that case, He spites arrogance by giving it false security, just as Paul says. This is why Jesus, in a similar vein, denies any miracles to the unbelieving Israelites (Matt. 12:39-42), even in his hometown (Luke 4:23-27), knowing that nothing will convince them from their ways (Luke 16:27-31). He goes even further in John 6 by essentially shooing away a crowd who were simply ecstatic at his physical rewards of food (John 6:32-67). When Jesus did miracles in front of unbelievers, they called him demon-possessed (Mark 3:22).
For this same reason, God not only won't carve any Ten Commandments on the Moon, He'll happily oblige someone who doesn't care about the truth to think they've figured it all out (Rom. 9:22-24). It's not so much He's placed our importance so much lower than His own: Jesus happily associated with the low classes of society of his day - and these weren't unjust labels, these were people who made their own choices to be drunks and prostitutes (Mark 2:15-7, Matt. 21:31-2). But these people, just like some of the Pharisees (e.g. Nicodemus), turned to Jesus. Would you disrespect yourself and waste your time trying to convince someone you know has repeatedly broken their promises and your trust if you knew they wouldn't heed your advice (Matt. 18:17)? Or if someone was pushing you to do something for them instead of asking, are you going to do it, knowing it's pointless? In the parable of the unjust judge, the widow was demanding something that was hers; here someone is demanding something that's not only undue, but will be wasted. We're not omniscient like God, so we shouldn't stop trying, but God has no illusions about the forever stubborn. And the opposite for believers: strength through weakness (2 Cor. 12:7b-10), the wise who reject Jesus defeated through foolishness (1 Cor. 1:18-31).
And imagine, if Jesus was unwilling to oblige the unbelievers of his day with miracles because of their insolence and obstinancy, how much less so would God today with that same person's complete trust and reliance on technology? That's not the purpose of miracles at all. There's a folktale of the Bulgarian chronicler and national hero, Paisius of Hilendar (18th century). Some youths went to, maybe derisively, ask him to show him a miracle. He pulled out a big sword and said, "Let me cut your heads off, and I'll glue them back on after." They all ran away. Miracles require faith and a purpose. Not so someone's curiosity can be tickled.
The Bible doesn't give miracle-workers some kind of superhero status. It's a reflection of their piety, sure, but it's never anything other than a tool. Paul mentions his own in passing (Rom. 15:19, 2 Cor. 12:12). In fact, aside from the Resurrection, the only one he elaborates upon isn't even his own (2 Cor. 12:2ff). Acts only notes a few of his miracles. Jesus says others will do bigger miracles than him (John 14:12) and denounces those who call on his name but don't do God's will, even if they were miracle-workers (Matt. 7:21-23, particularly verse 22). Similarly, Saul and his men, in the midst of his murderous hatred and pursuit of David, are stopped by God's Spirit and prophesy (1 Samuel 19:19-24).