OK, after thinking about this from many angles, it seems the crew aspect may hold the key.
Crew mates get the loot they deserve, and those not in crew can either request crew or go away.
Only crew share in the "crew loot" & benefits (of crew) unless they've been actively shooting or repairing the ship, whether they are in crew or not.
Anyone in crew found not to be helping can then be booted from crew and still stay on the ship if they choose, getting the loot they actively helped to earn, be it sinking ships or repairing the boat.
Those that do nothing and get booted from crew would get nothing, but can remain on the ship if they choose to.
Those that do work and get booted from crew for some reason will still get whatever they earned by helping.
In this scenario, even if you get booted from crew unfairly after having helped out, you still get your loot and don't have to worry about it or about getting booted off the ship unfairly.
If you did nothing, you get nothing.
No one gets booted unfairly or robbed of their good work, etc.
Moochers can stay on board and if they do nothing, they get nothing.
However, the limit to how many pirates can be on a ship should be related to how many active crew mates are on board, not how many pirates there are on the ship, as those not working do take an active slot away from the pirates who are actively playing the game.
So, if a ship has 12 slots, those in crew should make up that tally, not those not in crew or doing nothing.
While there would still be a slim gray area for those who worked and then got booted from crew, those players would still get all the loot they helped or continue to help earn.
No one gets booted unfairly or otherwise, and no one who earned loot gets robbed of their loot.