What people seem to be missing is that it's not as simple as "oh it works in homebrew". It does, sure, but then you have people saying it's at "near perfect" speed. Near perfect is not enough for Nintendo.
Nintendo want the games running as they did (if not better) than on the original consoles, and having it be "near perfect" is an issue. Then there's the Virtual Console features. Just throwing the GBA binaries on the handheld and selling them would be terrible, especially as they don't activate sleep mode when you close the 3DS.
There's also the issue of accuracy. This article will explain why it takes a 3GHz PC machine to accurately emulate a SNES.
http://arstechnica.com/gaming/2011/...-3ghz-quest-to-build-a-perfect-snes-emulator/
People say it'd be fine as they can get them working through other methods, but can you imagine the hell Nintendo would get for releasing imperfect Virtual Console releases with speed issues, accuracy etc.? Nintendo want to get it as close to the original as possible and cutting corners just to get them out is not their style.
It's not just a matter of "SNES has XMhz but 3DS has X+YMHz so it should be running better". It's not a straight conversion. The consoles had different architecture which is why emulation is necessary.
As has been said, the NX...both handheld and portable are said to absorb Wii U architecture and run the same OS with similar architecture to eachother. As such, developing the Virtual Console further for the 3DS and N3DS to try and get SNES working, especially as the 3DS has less life ahead than it has behind, is a waste of resources. By putting the focus on the Wii U, they'll be far more easily be able to have it run on both the upcoming handheld and home console, possibly even completely at launch which has been hinted by Iwata