If I recruit my max number of pirates, send them exploring, then hire more pirates in the tavern, when she ship returns (still full 'o pirates), those newly-hired ones in the tavern vanish. I'm not sure if it's a bug or design (I'd lean toward the latter), but I figured I'd report it, just in case.
It's not a bug and the ones in the Tavern never vanish. When you unload the ship after a voyage, if there is no room in the Tavern for them, then those are the ones you lose. If you want to move the crew from the ship back to the Tavern, always make sure it's empty, or at least has room for them, before doing so.
Thank you for the (quick) clarification, Chris. Just curious, what substances are you consuming to be able to stay on top of all these posts?