Or they can have the Nova Corps co-existing much like the GLC coexisting briefly with the Darkstars and LEGION before Emerald Twilight.
As for Arthur and Namor, Fantastic Four introduced another Atlantean city that stayed hidden for centuries. They'd have to do something similar, with both Arthur and Namor coming from different cities that comprised Atlantis and stayed separate through the years. Perhaps the cities were at war at the time they drowned.
Yes I think it was Peter David's Aquaman that said there were multiple Atlantean cities with Aquaman's Atlantis just being one of the most powerful states.