I'm probably more of a conventional thinker, as I'm currently studying history in University, but I wouldn't rule the prospect of the existence of Atlantis out. Though the evidence of Atlantis existing is inconclusive, that also means the evidence that it didn't exist is inconclusive, meaning, we don't know for sure.

It's also important to note, that great empires during that time frame, pre-3000 BC, weren't that large. Ancient Egypt, the greatest empire of its time, was quite small compared to what we consider great empire to be today. So the idea that Atlantis, a great empire of its time, was probably pretty small compared to what we consider to be a great empire today, so operating under that assumption, its quite feasible for an empire of that size to be completely wiped out in a cataclysmic event.