I really doubt that Warioware was actually emulating the Starfox ROM, much more likely it was coded from scratch for the game.
DKC didn't use the SuperFX chip, "ACM" just means that the graphics were pre-rendered on SGI hardware and saved as sprites, which the SNES is quite capable of displaying normally.
Emulating a game with a Super FX chip isn't that much harder from emulating a regular SNES game - the SNES does have 5 processors, after all. A "lack of Super FX hardware" is no different from a lack of a SNES CPU or Mode 7 chip on the Wii. SNES emulators for the PC have gotten games working that use Super FX, C4, DSP, and all kinds of other add-on chips. I wouldn't worry about Nintendo not being able to emulate those games.