Yes, this is a known issue. It's a fault of the emulator being used. Ugetab discovered this years ago, which was a contributor to why he stopped riping USF files. The more recent versions of Project 64 (64th Note uses an older version for its emulation core) fix this problem, but since the newer versions are closed source, the problem hasn't been "fixed" (it's also very possible that 64th Note's code is incompatible with newer sources, and would require a massive rewrite to get it to work).
Being that it's an emulator issue, it almost certainly effects other USF sets, but it's just more noticeable with Zelda. I'm fairly certain that a fix is wanted, but getting working N64 audio code (and getting it integrated into 64th Note) hasn't been easy. Though, I have no doubt that people here are open to suggestions, if you have any.
So, in short, it's a known issue, and is difficult to fix. Hopefully that's helpful. Mouser X over and out.
Oh. Like you say, it affects some other sets too. I remember Starfox being one of them. At first i thought the rips were from the 50hz PAL versions and thats why they sound slower (i assumed many PAL versions also have slower tempo, but it turns out its a rare thing that happens to crappy conversions like Sonic 1)
Anyway, i tried to use a plugin in winamp that allows you to play with tempo and make it faster/slower. But when i use it with USF rips it crashes.
Other games with this tempo problem include Super Mario 64, Mario Kart 64, Yoshi's Story, and Donkey Kong 64.
Interestingly enough, DK64's usf files play with a slightly lower speed in Winamp but play normally in Foobar.
@Soulis: What plugin are you using? I've been using Pacemaker to regulate the speeds and that almost never crashes Winamp.
I suppose one way around this is to create custom brstm files either from the music played in-game (most likely through a music modifier code) or from an original soundtrack CD. For DK64, you could try ripping mp3's from the files via Foobar and then make brstm's out of the mp3's. This method could eliminate your dependence on plugins with occasional annoyances.
Sorry for the late response, i was using the same plugin but it crashes for me when i use it with USF files. Maybe i need a different version or something.
Edit: Well, it seems i had an older version, the one i d/l now works. But it produces some very slight, hardly noticeable sound errors that are noticeable enough for me. So, again, i can't use it.