Epicenter, look at Neo Geo - system much much more powerful than MD. NG had Zilog Z80A for general sound operation, FM chip: Yamaha YM2610 15 Sound Channels - 7 Digital, 4 FM synthesis, 3 PSG, and 1 Noise Channel. This IS a bit more powerful and tricky to emulate, isnt it? So why we haven't problems with NG sound in emulators? neoragex, kawaks, even gp2x ng emu sounds wery well ?? With beefier 12mhz M68K CPU to emulate, not to mention much more advanced video processor...
It's not an issue of speed, so I don't know why you're even mentioning the graphics hardware or CPU clockrate. The issue is accuracy to original hardware audio. At any rate, there is less noticable inaccuracy of emulation of the NeoGeo's audio to the MegaDrive's because most NeoGeo games produce the vast majority of their sound by playing a series of pre-recorded ADPCM data. If you strip that out, there is very little FM actually being produced by the YM2610-and-company. Most MD games use a bare minimum of PCM samples, if any at all, and rely on the YM2612 and PSG for all of their audio.
At any rate, adding more channels really doesn't make it harder to make the sound more accurate, just more stressful. Once the concept is down and the chip is understood, it's trivial to just emulate more channels. The problem is fundamental. It will never sound as good as the real thing will. It can come pretty close, like accurate NES and SMS/GG emulators do, but they're still not right on the money, and they still hog more CPU horsepower than the GP2X or any handheld emulation device has to offer.