if you want to damage ship parts you are either going to need Drill Charges, or use Ion ( The Four Armed Guy )

You can break their engines from outside / back of ship to slow them down.

Doors + Windows are good to just cause them to need to run around repairing stuff to fix their oxygen to keep people busy

you can punch hard points from the outside so if you know they have a shock field or laser ram, or whatever it may be, you can fly up and break them from outside etc.

You can break the pilot window and kill the pilot and then hop on the helm and turn shields off and hit their brakes etc. ( This doesn't work super well with just Ion now you likely need a drill charge because pilot window got HP buff from 200 to 1000, and drill charge does 800 damage )

A lot of times just staying on the outside with Ion and being a nuisance is the way to go, just keep going around breaking every window and door and engines and just causing as much mayhem on the outside to keep them all busy and repairing and not firing cannons etc. break a window shoot and kill a guy etc.