/me actually has never played Mother 3. He still believes there will be a port, and as such has not emulated it.
But yup, the thing is, EB/M2's world is a parody of the USA (it's called Eagleland), and thus it uses lots of pop culture references, including bits of music like Zeny said (I'm pretty sure the Runaway Five as a band was based on something real). It's easy to think that they could just change the music a bit, but for one, it's a good chunk of music, not just one or two songs, and two, the songs are part of the whole America parody thing; changing them would dull the original point of the game.
And there are some other things as well, I can't recall everything there was. But Nintendo was pretty much bombarded by copyright-related lawsuits, and there's no way they want that to happen again if they put it on VC. And you can't blame 'em ;o
It's kinda sad though. John Lennon, one of the Beatles, sang a song called 'Mother,' which Itoi has said was part of his inspiration for the series. Then EB comes out and in a way pays tribute to the Beatles, but it gets attacked by lawsuits instead of appreciation :<