Why the pirates didn’t boot the captain could be their undoing. And losing the navigationals? Big mistake.
Possibly. Then again, John's attempt to blackmail the crew into mutiny didn't sit well and I don't blame them. I would have probably done the same thing.
Also, I get the impression that the winning crew of each expedition gets to pick a new captain, who in turn picks new officers. So there is no guarantee that J.D. will remain caption.