I'm wondering this bc I want to post my future runs on leaderboards but the Main categorys don't allow nintendon't.

Yes. Nintendont is in the same group as emulation, so feel free to run on it and submit your times. Just like with emulator though, once you hit a 1:05 you'll have to run on console if you want your times to be on the main leaderboard. The CE page has a category specifically for emulator, and you can submit your times to that also if you'd like.