No. They were decided when the entity in question was added. The last few added (CP ships) seem to be some of the best room-ship wise. For instance the ARC-170 has 3 rooms, while most fighters only have 1, and the YT-1210 only has 1. Just a quirk, though I think I heard one of the devs saying they were looking at fixing rooms.
That'd be great, as I'm certain my PLY-3000 should have more rooms.
I'm curious, will adding more rooms to lots of different ships cause lots of server load? Will they be looking to add more rooms to most of the ships, or will they have a maximum number of rooms they can use without overstraining the server?
Also, what if items are in the room of a ship that is removed after the change?
If I like the way the rooms in one of my ships are laid out, can I choose to keep my old room layout?