Nintendont is considered an emulator, since it's not official, but on the other hand, if you're playing directly on your Wii with the Zelda Collector's Edition disc, it doesn't matter - it's more Virtual Console than emulation. In any case, emulators are not penalized at all, for the time being.

The timer starts when you click on "play selected world", and ends when the second TNT explodes. I prefer to keep the word "glitch" because it's more common in the speedrun world, but there's no Minecraft glitch as such.