So I was doing a bit of honest pirating just now, I manage to board the people in question and secure their sinking, but I lost my own ship in the process. They had some skulls on board, so I mark the map and sail back, no skulls floating and water was to deep to go down and find them.
Solution is simple, make loot float indefinitely, or add in a sea floor that we can swim down to so we can recover loot.