Since all the NPC's use "Captain" and a random name, no player should be able to set their name up the same way. It's basically a person exploiting the name standard so someone things they are an NPC instead of a player. Either that, or make sure the NPC tag is on the ship, and the highlight box when you mouse over a ship has an obvious different background.
OK Ben a graphical way of identifying AI captains had actually been our first choice and limiting the name the second choice, so that will work fine.