It shouldn't as long as your music in iTunes is mp3. If they aren't then you will just have to use iTunes to convert them to mp3 and then add them to his player. It will create another folder instead of overwriting the current one. Once the music is on his player just delete the additional folder.
Again, it shouldn't. At least on the mac side everything in in it's own directory structure, and Zune will want to import(i.e. copy and convert to wma format) them. It may not be able to convert them all, but it shouldn't delete them.