IIRC the SVN core setting is indeed messing up some things, and won’t go well with Win98. It’s rather experimental, and necessary for things like save states, but I would keep it disabled whenever possible.
But it shouldn’t affect sound at all. I found that for really clear sound, especially MT32/MIDI, you simply need to set mixer and soundcard frequency to 44100 or 48000. At 22050 or lower, sound is garbled. These higher frequencies should also have zero impact on performance.