Nothing much? It's just two 2A03s and two RGB PPUs all running off the same clock. The shared memory and IRQ handshaking is the only weird thing, and that's probably only hard with emulators that use catch-up optimizations.
If I had to guess why it's so rarely emulated? There's only six Dualsystem-requiring games
according to Nocash and Wrecking Crew is probably the only one that's compelling to western audiences...
In fact, since the two PPUs are running off the same clock, and /RESET for everything is tied together, and it's the RGB PPU, there's no missing pixel, so the two PPUs should stay genlocked forever, too.