You can replace sound files just like textures by putting them in your custom pk3. Just locate the sound(s) that you want to replace in the data-1.1.0.pk3 with a zip tool. Then save the new sound(s) in a temporary direcrory under the same name and the same directory structure as the ones you want replaced and zip that directory into a zzz-mysounds-0.0.1.pk3.
Copying sound files into a mod (and distributing that mod of course) is always infringing on copyrights unless you have a license to do so. If you don't know the license for a file, then it is probably not free.

Of course you can always distribute sounds created by yourself, but if you do so please add a short textfile to the pk3 that contains the author and the license terms for your sounds.