But here's a problem that no-one seems to have mentioned:
If Atlantis rises from the depths -
which people are living on it? Clearly "normal" people (i.e. bipeds with lungs that breathe air) couldn't have existed on Atlantis while was under the sea. Therefore, they must have adapted by growing webbed feet and learning to strain oxygen out of the water (not to mention the problem of seawater getting in their noses and eyes).
For thousands of years they'd been under the sea, and suddenly Atlantis rises into the fresh air again.
Whatever people are living on it - "normal" people, "undersea" people, or even Cthulhu-esque "minions" (maybe?) - they would not be accustomed to such a rapid change. They would need time to adapt. Someone who can breathe under the sea, but not in the air, would asphyxiate (see fish). No wonder fishermen hit fish over the head when they catch them. It's less cruel than letting them die of asphyxiation.
Getting back to Atlantis: how do these people adapt so quickly to living in the fresh air? Never mind asphyxiation - there's a huge change from living in the dark, bottomless sea to living in the light again. It would be like staring into the sun - unless they keep their eyes shut tight (and how would they know they had to?), they would go blind from the experience.
The change from "straining oxygen from seawater into their eyes, noses and mouths" into "breathing oxygen from the air" would also be problematic. Generally speaking, oxygen in seawater is cleaner and purer than oxygen in the air. We haven't
quite polluted the sea - especially deep underwater - as much as we have polluted the air.
Hey, no wonder some people go off into the middle of the sea and try to found their own countries. The air is cleaner there!
And we call them crazies and kooks.