If you want to stick with the game's current system, each military ship should have a modular setup of stern, middle, and bow. Each should have different, but balanced, selection of weapons and utilities slots. These sections are completely separate files, just governed by a text file for combinations.
To use the DDs as an example. Here we would have to have Berkeley's stern project those intakes along the centre section and tweak the other designs a bit to make the cross sections along the cuts the same across all three (Lancaster's intakes being the biggest problem, may just have to make them a lot shorter). Then the difference kicks in with the weapon slots. Amatsukaze's bow seems to have loads of small slots, Berkeley's has fewer but larger slots, Lancaster has both few and small, so would need to take extra/larger utility slots to compensate. The centrelines have a stack of missile silos for Berkeley, a hangar (?) for Amatsukaze, and lancaster looks like she's taking utility slots again, and so on.
If you want, I'll take a look at separating silo points from turret points, which would be far more in-keeping with this universe.