I can confirm this affects different servers to different degrees. On my linux server, I ended remastering and renaming the standard quake sounds and moving them into a new folder. Another member and I watched as 1 quake sound at a time would stop working on his Win32 server; they're still broken.
The testing on my linux machine was with sv_pure 0 and no pure_server_whitelist.txt file.
I do have the attached files below in my orangebox/cstrike directory.
I haven't seen anyone mention these file yet. Are they replacements for the pure_server_whitelist.txt file?
What I observed was:
1) I had sounds under misc that DID work
2) Any sound under quake would not work, including one copied from item 1 above
3) When I copied the quake sounds to a new folder, some started working.
4) When I remastered and renamed (don't know if rename important) the broken sounds, they all worked.
I hope this is just some weird bug that gets fixed and not some Gestapo move.