Originally Posted by Couchpotato
… due to the world evolving 100's of years from medieval to the renaissance era technology.

Huh? Risen 2 is set "only" ten years after the events of the first game. The hero is the same guy.

That and the gods are all dead who were the source of power.

They were already "dead" (or actually they abandoned the world according to official canon) in the first game so that does not serve as a viable reason for the absence of crystal magic.
You will, however, be able to learn Voodoo magic so it's not like there is no magic at all in the game.