The Control Room allows the ship to move and receive commands. A ship with no Control Room cannot move. Weapons fire at will.
Since crewmembers do not have rank, and are alike in appearance and ability, any member of the crew can become "captain".
The destruction of a ship's Control Room will invariably lead it to the destruction of the ship itself during battle. It is for this reason the Control Room should be kept far away from explosive ship modules and protected by armor, a shield generator, or a point defense system.