i would love to see signal flags. it just adds to the immersion. as i previousely mentioned in the flags and ensigns thread: i dont know what the officers slots are good for, but if officers are implemented for e.g. seperate gun decks, sails, marines, etc., having a signal officer would be a nice addition. depending on his skill/level messages could be transferred/understood faster and misunderstanding of signals reduced. also this would challenge the player to learn at least the simple commands, simply to check if the message is understood right. distance and smoke could also make it hard to read signals, so that one would have to guess what it means.
i wouldnt make it a priority but definitely add it to the to-do list!