This game is also available on the wii, is it safe to speedrun the wii version?

Correct. It is.

Hi, I actually own this game on the Wii and in the campaign the mission "Black Cats" doesn't exist. I was wondering If I submitted a Any% run on the Wii would it be accepted? Since "Black Cats" usually takes around 11 and a half minutes to complete optimally. Meaning that the Wii version would save 11.5 minutes because it doesn't have "Black Cats" in it. Would it have to be its own separate category?

8 months, still no answer... :/

Sorry about that, a wii category has been added, you can submit any runs you do there, it's under misc.