Welcome
Conning Tower does not show damage, its a Stock thing\issue ( there are however some great Damage Mods out for the rest of the sub ), the flak and deck gun do show damage, twisted, etc. Unless the hull was breached you would have no flooding, I have had my Conning Tower blown to bits, but managed to make it home or to a friendly port for repairs.
As far as Flotillas, as the war progressed they were created to address Germany's War Needs\Strategies ( later in the war they were forced to move to other locations as well ).
uboat.net is a great site for all things U-Boat. Flotillas all have their advantages, disadvantages depending upon how you want to play the game, where you start a career

, what type of boat you want. Not sure about the Bergen thing:hmm:
Plus if you are not using SHCommander, get it below. There are a number of cool things you can do with it.
http://www.subsim.com/subsim_files/patches05/SH3Cmdr27.exe