I should mention that I have since seen this done before, with Xerecs and his brothers having a “sub-ocean” in their CoEC 2021 game.
It would be hard to pull off in “full”, especially if more than 2 total layers were desired. Ex: the normal surface, the “underwater” area where subs drive around and sea creatures swim, and then the ocean floor where shipwrecks and random objects/artifacts lie (such as cargo tossed overboard due to illegal situations!). Having enough space for hands to move above ships would be tight, and it would be just about impossible without either sliding surfaces so you could pull out a sub-layer to access it, or a standing game where the main surface was above regular table height (such as ~4 feet high) to ensure room for the other layers.
Of course, if you went all the way and actually did this in a (preferably) big or huge game, you’d want to make it worth it – submersible customs available, and probably a bunch of house rules so that “sunken” cargo and even some ships would be somehow available to salvage/loot/etc. Maybe a way for The Cursed to come back from the grave ala PotC….