I'm pretty sure that the units in the ship are killed when Guybrush (or any other unit with boarding party) captures a ship. Of course, arcane barges can still be captured, and I think that unit with waterwalking (even if loaded in the ship) will fight to defend themselves.
You could put Guybrush on a boat and capture boats in enemy territory.
Hmm...how about making a Lanun-only, unitcombat_naval only a spell that lets them sell captured boats away to other pirates to gain gold? And maybe turning the ship barbarian instead of just deleting it. I may add this to my modmod.