I think you hit on quite a few interesting facts/ideas. Numerous civilizations, some relatively advanced, have come and gone over the past 10,000 years. If the attached chart is reasonably accurate, modern man (Homo sapiens) has been around for at least 100,000 and possibly 500,000 years. Considering how far man has advanced in just the past 10,000 years, it would appear that there has been ample time for multiple advanced societies to rise and fall. Hence the opportunity for multiple Atlantises with remnants wiped away by time and the occasional meteorite.

As to your plague comment: I recently read that archeologists excavating graves from the Roman period came up with an interesting discovery. They were able to extract DNA from 19 sixth-century skeletal remains indicating that they had succumbed to "the plague". So, the Black Death of the 14th wasn't an isolated event. In fact, it may have been a major factor in the fall of the Roman Empire since a weakened population couldn't hold off the invading Huns.