I have no idea what you said in the second sentence, but pretty much all Vc emulators are made to run just that game. Which means they don't bother with mode7 emulation on any snes game that don't use it, for example.
So if a game uses something no other game available uses, than the emulation will not work because why bother emulating that feature if this game don't use it ?
While each individual game has got emulator settings tweaked for minimal madness, I really doubt they optimize the emulators to that level in case of all games. Though I am aware they are merging the roms into executables for NES/SNES titles on Wii U.
You may be familiar with concept of NES mappers, the cartridge parts doing stuff - as well as SNES cartridge chips doing other stuff. This is surely something they only support to some level, it's not truly surprising as anything could be theoretically put on a cartridge, and they don't bother with bootleg games and such.
DS does not have that in general (though there are carts with IR ports and some unofficial flashcarts have extra processors), but it has two CPUs - at least the first iteration does, there are rumours that DSi added another one, and 3DS surely did for its own purposes. Now if it was a 32X that would just make emulation harder, but the fun part is that Nintendo apparently didn't allow third party developers to use anything but their standard support program on the older of these, this support program got updates but there is a somewhat limited amount of versions. You can draw parallels with Wii IOSes running on the so-called Starlet or N64 graphics core "microcodes"... or with mappers, though it's software, not hardware, this time.
So one could write an emulator which instead of emulating the second programmable unit in the hardware attempts to clone behavior of a specific program running on it instead, which would be faster. Dolphin does it with IOSes right now. A lot of old N64 emulators did it back in the past and I think the popular fast ones still do - it does help that besides few outliers from RARE and Factor 5 apparently all commercial games used the same or mostly the same auxilliary program here. I think it is actually an unpopular approach on DS emulation because homebrew programs tend to put varied things on the auxilliary core, but Nintendo is not emulating homebrew and Wii U isn't too fast so I am wondering if they did this as it would limit the compatibility with injection of software that used a different version of the support program.
