only someone who has access to the Jedi Archives could deleted Kamino from them, so i suppose that Dooku deleted the system and he or Palpatine order the clone army
in my opinion the sith lord will be more than 3, i dont konw why its only an idea, since the game is called "The Sith Lord", but yes, one of the possibilities is that Bastila is the third sith lord, i dont think so, but everything can happen...