As a matter of fact, it is advisable to disable "fixed audio timing" in every single game and just use a third party audio plugin to fix sound pops. Fixed audio timing screws up frame rate and causes unstable VI/s. Stable 60VI/s should be the norm for all US roms. Fixed audio timing causes it to go anywhere from 58 to 62, which should make your games stutter more than they normally do.
The same could be said for the VI refresh rate value. If you look at PJ64 1.7 settings, 1500 is the default. This value is also the default one in Retroarch's Mupen+ core. And since 1500 also fixes the timings/speed in many games on PJ64 2.0 (not just Zelda), i'm pretty sure it should be the default, correct value.