What sort of evidence would you expect and find to be missing? It's referred to in the literature, e.g. Appian, Civil Wars, 1:120 tells how Crassus crucified 6000 people at the end of the Third Servile War.
What evidence could you expect? (This is just a list of some possible evidence and why or why not it's been found).
Nails. Nails were often reused, so there weren't many and are unlikely to be found still in a skeleton. Nails were also rarely used in the first place, rope being preferred for the wrists, so the chances of finding nails are reduced. Nails may have been used as protective charms when used in crucifixion, so if we find a nail, or part of a nail, as a charm, we could, maybe, think of it as evidence of crucifixion, but that would be very tenuous evidence tbh. Nails are not the best place to find evidence for crucifixion.
The cross. Crosses were made of two parts, the stake, which was in one permanent place, and the crossbeam, which was what was attached to the individual. We would not find one whole cross if we looked, just a beam and a long pole essentially, and they could be used in anything. That's if the wood even survived, which is unlikely. Perhaps if it was specifically placed in a swamp, there would be evidence, but the chances of that happening are almost impossible, so there will probably be no crosses found, or parts of crosses. Rope used in crucifixion will also not be found for the same reason, along with the fact that we wouldn't be able to tell whether rope found was used in crucifixion.
A body. Now this is something that we do have. Remains of a victim of crucifixion. In 1968, Jehohanan, son of Hagakol, was found in an ossuary outside of Jerusalem. His heel bone had a nail forced through its side, the point of the nail having fragments of wood remaining from the cross. But this is our only body. Most bodies were simply left to rot on the cross, or left to decay close by, the ultimate humiliation and warning, so their remains would not be found. Added to that, the chances of finding skeletons are still slim. The odds of finding a skeleton which had undergone crucifixion are tinier. It shouldn't be surprising we haven't found more crucified remains, rather it is surprising that an archaeologist even found one.
Literary. We have a ton of contemporary literary evidence of crucifixion in antiquity, from Herodotus to Josephus to Seneca. Josephus even mentioned three friends who were crucified, using his connections, he was able to have them taken down, but only one survived his injuries.
Crucifixions are not just a thing from Antiquity, having been used in many places, and still used now, with evidence of IS, Myanmar, Yemen and Saudi Arabia having used it, as examples for occurrences within the last 15 years, and it is still a legal punishment in a small minority of countries. We have photographic evidence of the Japanese use of crucifixion, and written eyewitness accounts of Burmese crucifixions in the 19th century as well.
So for crucifixion in Antiquity, we have little archaeological evidence because there wouldn't be many remains of anything used in crucifixion. However, we do have a skeleton showing evidence of having been crucified, and multiple contemporary accounts describing, debating or explaining crucifixion.
For crucifixion as a whole, we have a ton of photographic evidence, court evidence and eyewitness accounts, and I believe even videos of IS atrocities. It's horrible that it managed to last for so long that our evidence for crucifixion ranges from a skeleton thousands of years old to phone footage.
As far as physical evidence, there are the remains of Jehohanan who was found with a nail through one heel; the actual mechanics of how he was crucified are a matter of debate though. It's thought (here for example, which also has a lot of useful journal references for further reading) that one reason there is little archaeological evidence is because prisoners were often tied to the cross rather than nailed.
I think a Historian/Archaeologist would have the answer the following question first. How often were criminals buried after crucifixion, rather than left to decay by the roadside?