Do some more in-depth search on your setting and you will get more answers to your question then you think. For starters, in WW2 a lot of ships were carriers - they boarded planes Look up the U.S.S. Enterprise. You would get lots of technical references from there. For example, you could build an airstrike against an enemy ship - draw out the hit trajectory and a couple of seconds later - boom, an air strike. This is just an example.
It really depends on your own design in the long term. How realistic and time period correct do you want the game to be ? How accurate ? By the looks of it, I'm guessing, pretty close to the real thing, though are you in for some technical tweaks and strays from the time period ? I'm talking stuff like having planes, carrier style, on a larger battle ship. I'm talking about having really high level artillery on board, mostly equipment that you would expect to be found on different kinds of ships.
If you don't feel like going a bit overboard and want to stay accurate, just look up some vessels from the time period and see what they had in terms of tech and firepower. Look up the tech and see how you can turn it into a gameplay mechanic. You most certainly don't need to fire guns, rockets and underwater missiles the same way, so you can maybe think of different handling techniques for different fire types.