Well, here's what I think. I'm going back to Super Mario 64 DS, where they pretty much used the same MDID sequence and synthesizer. However, knowing that this is a new platform built on it's graphical power, I believe they're going to perhaps update the synthesizer a bit in order to make it add on to the overhaul of the game.
A.K.A. They're going to have the same music, but they might get instruments better than the N64 version. My only issue, however, is that doing so could potentially ruin the nostalgic effect.