I have a GameCube with component cables and I use them on my 57" TV.
When playing the NES games in Animal Crossing, Metroid within Metroid Prime, or the Zelda games from the Zelda Collectors Edition disc, I don't notice a problem. Sure, the pixels on the sprites are evident. But that's part of the charm of retro games - and the pixels being brighter and sharper (and larger) don't take anything away from it, IMO.
I suppose it's possible for the Virtual Console to add effects to these games like some PC emulators do - adding TV scanlines, or anti-aliasing, etc. But to keep things simple, they probably won't.