Walt
Hi Walt, loving the game!
I don't have a solution for whole multiple levels, but would it be possible to have a single decked ship with Turrets sitting on top of the hull?
You'd be able to see them on enemy ships because they're sitting on the top, so could be targeted, but you could still armour your hull so you could, say, ram a ship without your guns being destroyed.
I built a ship with the ABH mod when I'd only had the game a few days (...still have!) and because I was trying to mimic a Star Trek ship, attempted to place Phasers where they should be, (picture of interior and the exterior), in the middle. Since Thrusters enclosed in the 2D plane work, I reasoned that the weapons might just fire over my own ship, but alas, I had to redesign... (Interior and exterior.)
As for seeing them on your own ship, they could be translucent, or, you could say that they need a room to service them from below, so they'd just act like any other room. It would still give you more flexibility in ship design without the complexity of multiple decks.
(And yeah, I've gone a bit crazy with shields...)