Can I use the virtual console version of Links Awakening to do runs? I have a big interest in running it but have no other way. Thank You!!

Unfortunately the 3DSVC doesn't seem to emulate the game accurately, so it's not allowed for the leaderboards.

That being said, there's nothing wrong with using it to learn the game or to just do runs for fun. Something to keep in mind, though, is that the VC version is v1.2 whereas we speedrun on v1.0 for most categories. So the run would be fairly different due to less glitches.