Um, I have no idea about the performance impact. I guess users will either use `root` in WebYaST or there will a single non-root user with all permissions or there will be more users but with few permissions only (just few roles per user). I don't think there will be hundreds of files in reality. 

One user/one permission per file make it easy when removing a permission, you just simply delete a file. With more users/permissions you would need to read the file, parse, remove not needed user/permission and write back which is more complex error prone.

I'd leave it as it is for now, we can change it later if somebody reports problems with it...