I didn’t do any ship battles until the endgame and then just equipped some vanilla superb armor and weapon on all of the off characters and did the same.
Overall, the ship battle system doesn’t work. I didn’t engage in any for most of the game because I didn’t have to, I couldn’t tell apart weak and strong opponents, I didn’t know what it would do to my faction reputation, and I didn’t know how many ship upgrades and crew levels were expected. And then I found out like you that the cannon minigame is meaningless and you should just board without choosing the immediate “board” option.
So it’s by far the most broken part of the game. Good music too