I have wondered this for a while. The anarcane ground may potentially have a positive effect for the defenders during the apocalypse, since the hoards of sranc were not so great, and the Consult needed the no-god to control them. Its possible that its walls and landscape are ideal for defending against sranc hordes.
As for why it would stand the test of ages, I have no idea. Like you said, in more recent years-of-the-tusk, the masses of sranc, I would think, would eventually ravage those walls. Without sorcery nukes to hold them off, it would seem like they wouldn't have much of a chance.
It could just be that Atrithau, just like every other human city, survives simply because the sranc have not be wielded en mass since the First Apocalypse. Sure they like to kill/eat/rape humans, but there isn't a big enough driver to band together and assault a fortress/city. At this point, if the Consult found some need to destroy a city, especially Atrithau, it probably could figure it out, but to what end? AFAIK, there is nothing interesting there, not even the Mandate proselytizing against the Consult on street corners. In the grand scheme, cities are nothing, especially when they are heavily infiltrated by skin-spies and the like.
In fact, here is a crackpot theory: Chorae are blind-spots to the No-God. That's why the carapace is covered in them and why he is constantly asking, "What do you see?"
Nice.