Atlantis gets destroyed almost as much as Xandar. I keep wondering where Namor finds the Atlanteans to fill the city with.
I suppose it's really easy to evacuate the city. For all intents and purposes, the entire population "flies" (technically swims). It's easy for them to scatter, and they're not limited to 2 dimensions and highways.
Plus, I'd imagine most Atlanteans are rural just like surface dwellers. We've seen various Atlantean cities over the years, and not just because they were getting destroyed. Just like surface dwellers have NY, Miami, Dallas, etc., Atlanteans have Atlantis (cities, plural*), Tha-Korr, Skarka, Amphitrite, etc. I'm sure they have farming communities and the like, too. Atlantis is a continent. Heck, it's more than a continent: it spans multiple oceans.
* "Atlantis" seems to be a very common Atlantean city name, and there are many Atlantises, like "Springfield."