All you need to do is give Battleships a webifier beam equipment (maybe built at pobs) that consumes energy when activated to slow target ship (gunboat and smaller) by some significant %.
Large numbers of bombers will still be deadly, small numbers of bombers will now be managable (and more realistic).
"Bombers force people to fly smaller caps" then what is the point of BS? If they're not good at killing everything, what justifies their slow speed and large size?