The Quarterdeck

When the ship is underway, the brain of it is the bridge, when it is stopped in a port the brain is called the Quarterdeck. Ask any sailor and they will tell you that the Quarterdeck is a necessary evil. When the ship is in port there are one or two Quarterdecks, one for officers and maybe a separate one for the enlisted. To cross a Quarterdeck you need to ask permission at least once, show your identification card, and do a version of a salute, depending on if you are in uniform or in civilian wear. People also have to salute the flag at some time, depending on if they are leaving or returning and if it is light out. All this tradition is based around reminding sailors of the rich history in the navy but the Quarterdeck serves a purpose as well. With only one or two exit and entrance points to the ship, it makes the ship easier to protect. If the attackers get in the gate, they still have to climb the uncovered stairs and cross the open brow to get on the ship, giving people on ship (there are always a few people armed at all times in port) time to stop the attackers.
I don’t recall seeing a space ship with a Quarterdeck in any movies or television shows and I would imagine that a ship would have a few safeguards against attacks, such as that they can fire at any shuttle getting too close to them or shoot any attacker accidentally beamed up. (I seem to remember a number of times on Star Trek episodes that the transporter operator was armed.) However, if space travel takes its traditions from the Navy, I find it hard to believe that the Quarterdeck will be forgotten, though traditions may change. If space travel takes its traditions from the Air Force, the Quarterdeck will likely be forgotten as it is mainly a Navy tradition.