I recently started trying to speed run this (however I probably will never have a successful quick time) and read the rules saying that 'Emulators are highly discouraged'. Does that mean I can still use them if I wanted to get a time? Or would I have to use a DS?

you can use them. just look at crrool's run. Just the use of Ram Watch (which would give u unfair advantage since u can see the rng seed you are on right away) is not allowed.