Since there is no in game timing, emulator is not fair to people who run on disc since it eliminates not only loading times, but lag in many of the rooms. An official disc is needed to run the game! =]
You can still run the game on emulator, nobody will or can stop you. The times just won't be accepted to the leaderboards, which really shouldn't even matter anyway. There are runners who run on emulator and have fun with it, not being able to submit to a leaderboard doesn't effect how much fun it could be. Personally I would probably run on emulator if I could actually get it to work as well as the actual game does. I still run the game from time to time and I haven't submitted to the leaderboards since last year. Really, as far as these leaderboards go, on the main category alone, at least 4 of the actual top 10 aren't even on there anymore, if they don't care, you shouldn't either.
Here's a somewhat relevant tweet to the situation: https://twitter.com/allspeedrunners/status/670438410759356416