Actually, the GBA one was pretty much a direct port of the NES version.
And you're missing the point. Each version is a re-release. The average user doesn't know or care if it's emulated, just that in the end, it's Super Mario Brothers.
So if Nintendo wanted to slap a 3DS label on a few of their older DS releases, they will, and people will buy them. So what if you won't, there are other suckers out there.
Getting back to the topic, though, I doubt that if Nintendo was going to convert older DS games to 3D, they would do it for free via firmware. They're still selling the DSi..... why shoot themselves in the foot like that? If they do convert DS games, they'll sell them in new packaging.
And a homebrew 3D upscaler for DS games won't happen until the 3DS is spread open more than a Penthouse centerfold, if even then.