I was looking to try to learn to run any%, but I wanted to make sure it was ok to submit runs from my SNES mini using the built in Canoe emulator. And while Canoe is not listed as forbidden in the rules, I'm not sure what version it is or where I would find that info.

So is there any issue with this or does anyone know how to find the version of Canoe on a SNES mini?

Since it seems to be the custom Nintendo emulator, I suppose it should be OK to use Canoe for speedrunning. Unfortunately I can't help you much with how to get it / set it up...

It actually depends on the speedrun moderators. They usually allow the SNES Mini option in a game that isn't official Nintendo. You'll have to talk to another moderator about that. They haven't caused any problems, but it's considered an emulator, not an official SNES Mini.