I think you are confusing Naval Bases with Shipyards.
Naval Bases are not used to build new ships, but as proper staging areas for a nation’s fleets with some repairing abilities and most importantly as supply depots to replenish the fleets.
Shipyards are where they actually construct new ships. In this game, Industrial Complexes are used to represent any and all types of new unit construction facilities. Shipyards, aircraft manufacturing plants (fighter and bomber), automotive plants (tanks and mechs), armament plants (artillery and AA guns), ammunition plants and recruitment and basic training facilities (boot camp) are all wrapped up in the single piece of Industrial Complexes for simplicity in this game.
Could you imagine if we had separate units to represent each unit’s construction? That might make SBRs almost useless. I mean, say your enemy comes over and bombs the crap out of your tank factory. You could decide that you just won’t build any tanks and hit him with more infantry and artillery while not spending one precious penny to fix the tank factory. And what if that SBR on your tank factory cost him/her a bomber from AA fire? All for nothing.
While I see the logic in your idea, I don’t think it is a workable project. Especially your Option #3. People already don’t want to buy naval bases, they sure won’t want to spend an extra 2 IPCs per ship to place them there.
Also, variance brings up a good point. Take Egypt for an example. It’s already hard enough for Italy to go after Egypt or even do much in the Med with their navy. If England could keep dropping 3 ships per turn there in SZ 98, the Italian navy wouldn’t stand a chance.