I recently visited the park only to find that the Action Theater was still operating. I thought all the Nicktoons were gone. I know this sounds like a ridiculous question. I just really wanted to know why. Is there an extra license? Did the park still need something to still operate in that area and closing it would be a waste?

Overall I still enjoyed it, I was just surprised as all to see it still there.

Yes, the license to play Spongebob 3D is a separate license. Many Six Flags parks play or have played it, as do many smaller parks from different chains. It has nothing to do with the Nick license, though I think it's playing at Kings Island and the other Paramount Parks was more than just a happy coincidence...