In Assassins Creed when you see the credits have you beaten the game

No, it only means you followed the story to the end, but fortunately, you will continue to control Desmond, where he can freely reenter the Animus. In ACII you hear Desmond agreeing to jump back into the Animus 2.0 to play around near the end of the credits. At that point, you are free to roam Italy and locate anything in the game you have not yet found. Basically, both games become free play.