The idea of separating out huge parts of the ship is kind of silly to me. It makes much more sense to have automated detachable parts that are just mobile weapons platforms.
I suppose when you watch Star Trek you have to drink the production cool-aid that the most effective way to wage war is to use a lot of kilometer long barely maneuverable high surface area art-deco pieces with the most vulnerable areas jutting out on the sides and the command center directly on the surface.
There's no reason not to have it automated, if a raiding party can somehow get aboard and get hold of usable command codes they can control the ship whether or not it's automated. If *waves hand* designing your warships around dragging your living areas around with your combat units is a good idea, the Vengeance makes perfect sense.
For some reason I thought this topic was about the ship in Message In A Bottle that separates into 3 parts and runs its own attack pattern, probably because that is the first 'Automated ship' that comes to mind for me.