I seem to be having more issues since I have got newer computers with dual core processors and higher end graphics cards. I started to even have problems in Null DC (the dreamcast emulator). In Null DC, it was a simple fix I just needed to increase the size of the sound buffer. I'm guessing the same thing will fix this also. Some games I think are just written totally different for the hardware on the DS because some sound is excellent along with the graphics, but some games are running more hardware and operations or something.
But that noise is definately the same kind of thing I was hearing in Null DC until I found out about the buffer fix. Somewhere in no$gba there must be a line of code for that I'm sure.
About 5 years ago I first noticed problems in emulators. I accidentally discovered that using a pro sound card like an MAudio relieves the processors quite a bit. Audigy and all that stuff is a joke and waste of money compared to a good audio card. Unfortunately, I had to sell my audio card and monitoring speakers but if you can, get a real card and some audio monitoring speakers because they blow your head off and also sound good at lower levels. You don't know what you are missing until you can hear a large range of frequency with no noise.