Hello Fury! I've a new strategy for getting loot drops whilst at sea without filling up with those useless cargo crates.
I call it "Poaching". Think of it like you would think hunters poaching animals, they kill it, but they don't finish the job by harvesting the fur and meat. This is the same strategy only not illegal.
What you basically do is disable the flagship and then sail away, forget about it, and move onto a different flagship.
I don't see how this can be flawed in any way. (Unless this displeases POTCO and they make it so you don't get the loot drops if you don't board it).
Another note, I can't promise that flagships will drop something every time they are disabled. You probably already know this, but I'm just making sure.
Alright, that's all the info I have to offer. Happy hunting mates!