Either way, this will be a long project for you I assume after reading through the patreon page, and thanks for explaining!I think the biggest thing for accuracy that can impact performance is timing. How long it takes to run an instruction, access memory, etc. and also synchronization between the 2 CPUs. Right now there's pretty much no timing system in place (the emulated CPUs are running too fast, basically) which could actually make performance worse because the processor has to keep up with the faster CPUs. Trying to make the timing too accurate though will also degrade performance, because of all the calculations and such required to figure out how fast everything should be running. I'll have to find some sort of balance between accuracy and speed. I also have a crazy idea or two that might help with performance, but it might mess up the synchronization, and I'm not sure how big of an impact that will have yet.
Regarding the audio/thread issue in melonDS, honestly I almost forgot about that because I've been so busy with this new emulator. It's also hard to debug because it doesn't happen on my end. I'll try to look into it again before releasing the hardware renderer update, but I can't make any promises. I've always found libnx threads to be a little wonky anyways; I've had issues with starting multiple threads on the same core and with getting them to run at all on the fourth core (which did work when I first released melonDS, but somewhere along the line something external broke it).
The problem started after you fixed the dock audio, maybe you can make a version with the older threads if your time is to limited but I don't want to ask for too much