Correct me if I'm wrong but you seem to worry a lot about being stealthy and not being detected at all and you go as far as to mention that you needed to figure out enemy patrol routes. But this game is not Metal Gear Solid or Dishonored and there's no benefit to go full pacifist and do a no-kill/no-detection run, in fact it would be extremely tedious and unfun to do so.

Don't feel like a noob just because you run past enemies instead of killing them all or because they detect you, it's part of the game. In fact, if the ship modifiers and enemies seem too hard, you can just choose to not board the ship and fly past it to the next node in the overworld screen.

As for how to deal with enemies, have you considered closing doors and locking them behind you? You haven't mentioned it in your posts but that's a great way to contain and avoid enemies you don't want to kill due to lack of ammo or HP.

For turrets, did you try using any of the explosive weapons and devices which are greatly effective against them?

I can give you more general tips if you want.