I know this is a game and stuff might break if Capships are overpowered but
one port on a capital ship is just dumb it would never happen

Goliath should have at least 3 Trident at least 5

If invincibility is an issue just restrict grid or only allow energy weapons / mining beams in ports

its not like anyone is going to sit in front of a trident in a vulture
and the turn rate of capships is so slow that you are never going to hit a moving target

Drevent, have you played with the recent automate-able turrets yet? It sounds like you somehow missed the update to me!