Crew simply means people, if their are none left, the ship will just sit there disabled, unable to attack, so lets say the hall has 10000 armor but their is only 3 crew, target the crew for a fast end to the fight. Also the little dudes on the boat represent the % of crew left, so if there are still a lot of little dudes but only a big of ship, just kill the ship.
TLDR: target crew to avoid heavy armoured ships.
♥