I believe the GM is free to create whatever world they want. That is the point of RPG after all. The heroes having disappeared has only just occurred and no one is sure what is going on. I do not know how many of the villains exist, but I am fairly sure the main ones are still around. 

We are not taking this super seriously. I RP for fun. I do not really care if the continuity is broken from the various other iterations. Should the world blow up? Maybe, but what fun is that? If it is truly a problem then perhaps this is not the RP for you.