Just to summarize what I did so far

1. recorded some .ogg file
2. put the files inside funnysounds.pk3 file
3. replaced the original file with the new one
4. added new commands for new sounds inside funnysounds.py script
5. restarted the server

result:
when I write a bind for a new sound servers tells me
WARNING: couldn't load sound: sound/funnysounds/mysound.ogg
WARNING: could not find sound/funnysounds/mysound.ogg - using default

P.S. I removed some original sounds from the pack and renamed my sounds with the removed files names and edited the funnysounds.py file accordingly. But when I was writing my binds for the new sounds the original sounds (the ones recorded in the files which I removed from funnysounds.pk3 file) were played.

Ok I guess I figured it will not work this way because client also needs this workshop item with the sounds and it downloads it from the original location and not from my server.