Will it ever be acceptable to speedrun NG on the 3ds?

I don't see why it shouldn't be accepted. It is an official release by Nintendo and most leaderboards (Super Mario Bros., The Legend Of Zelda etc.) all allow runs to be submitted using the platform. It might just be a platform that the mods either forgot or are unaware of.

Hmm.. I was curious because it says the platforms on the left is "NES, WiiVC, NESClassic, Switch."

How would I submit a run if I were to do one on the 3ds?

I honestly recommend that you do try to run it either on original hardware or an emulator because all other versions run at a slightly slower framerate, which loses time over the course of a run. If you were to submit a run like this though I would recommend submitting it either registered as NES and check the Emulator box or submit it under WiiVC, but specify that it is a 3DS run in the description of the run. Hope this was helpful