Recently, Nintendo shockingly acknowledged Mario Maker 2's existance by adding a new ninji. My question is how will this affect the All Ninji's category?

Will all current submitted runs be removed or will the category remain the same and not include this new one?

probably will remain as current one they probably know about that idea and are not going to make a deal every time a new level cames

For now, we're not going to verify any new All Ninjis runs until we get this situation resolved. We're currently working on making a poll for the community to vote on though, so stay tuned for that.