An example of a game I cannot get clean audio with is Beetle Adventure Racing. The "beat" on the title screen never loops cleanly, regardless of whether sync to audio is enabled or not. Nemu64 plays the audio smoothly for this game. There are a number of other games that exhibit the same "jittery" behavior.
More complex games lik Zelda, Mario, Donkey Kong, Banjo, Conker, etc are all perfect so it just seems more like an oddity than anything else.
As far as FPS drops, I expect the FPS for n64 games to fall. They fell on the original console. I do however experience a strage "stall" for 2 or 3 seconds in Banjo Kazooie once every few minutes. I haven't seen that behavior in any other game.