I've started learning this game but it lags really bad on my computer and I find that it runs a lot better on my switch through retroarch. Is this allowed? It has different cores for different well known emulators but I thought I might as well ask here to be safe.

3mix has a lot of lag in the game even when run on an actual NES console. If something is reducing the lag the game is supposed to have, than that wouldn't be allowed, but if it's just fixing some computer lag you were experiencing before it's probably fine. Retroarc also uses the runahead feature that improves latency from controller to the game. I think that generally 1 frame of run ahead is accepted and 2 is considered actually faster than the NES.