Missiles were kind of OP against fighters in 85--I had a dual-torp gunboat and was able to 1-2 instakill fighters every once in a while. They also worked well when a fighter tried to shield-run since the missiles had good range. You could also use them to supplement CDs against bombers and mines sometime. On the other hand, missiles didn't work in close-up furballs, due to lag. And if you met a turret boat in your missile boat you were going to lose. So to me they pretty well balanced just a little bit OP against fighters. So to me the preferred tweak would have been to reduce hull damage so that it was not possible to instakill a fresh fighter, but you could still finish a shield-running figher. This would be the preferred loadout for my house gunboats that mostly interdict other fighters (my BH gunboat would stay with turrets).
As for use with deshielding caps... the only way gunboats will ever be a threat to caps is if the forward gun is allowed to be replaced with a torpedo launcher. That won't happen. Some of the turret-splitting changes did introduce blind spots on a few of the caps so it's possible to get up in the exaust on a specific ship and not take any return fire. That is something else though.