They should just make it so your ship saves whatever is on it when you disconnect or log out.
This would work with any item, except the fort key of course.
Now, of course there needs to be some sort of restriction, so it is not abused.
I was thinking, if any ship is within 500 meters of your ship, a warning pops up saying "Ship detected, logging out now will forfeit your cargo to the sea", and it would do exactly that, drop your cargo off into the ocean if you log out.
Also, if you have taken player damage on your ship within the last 5 minutes, you also forfeit your cargo, "Warning, player damage taken X minutes and XX seconds ago, logging out will forfeit your cargo to the sea".
If you disconnect, same rules apply, as to avoid people just pulling the cable out of their Computer/Xbox.
Now, this also have another advantage(Or disadvantage) in that all your supplies are not refreshed.
Which brings up another suggestion with this:
Supplies are no longer refreshed... EVER, you have to resupply your ship manually. Better stock up on those planks.
I am getting a little annoyed when my boat turns into a submarine or into an airship by this A***e called Allmondbeard, so it would be nice if it weren't a complete loss to disconnect.