I had a Dhow with all 16 crew slots filled when i did the quest to capture the Floating Hangman. The Floating Hangman only has 15 crew slots, as a result my Helmsman vanished. He isn't available in the known sailors list either, he is completely gone. Unfortunately by the time i noticed this, the auto saves and the quicksave from before getting the Hangman were overwritten and the last savegame i have is 11 hours old.
Well, that explains why GOG Galaxy permanently wanted to download an update yesterday but failed every time... I got an "update failed" notification every 15 minutes or so while playing the game