The Strategic BattleForce and Abstract Combat System supports WarShips. They are abstracted out more and have limits placed on them to be over powered (for example a Squadron is limited to one WarShip in its six Element make up).
Inner Sphere at War, which is the campaign system, does not support the creation, maintenance, movement or repair of WarShips in the base version. That won't prevent you from using them in combat in ACS and SBF.