I'm setting up a SLES 12 system for running web applications on it. There is already a /srv/www folder and it's going to be owned by a special user (let's say: web user).
Is there a good practice / standard in Linux (and maybe specially in Suse Linux Enterprise Server), what folder should be the home of the web user / web root owner? Should it be the web root itself?
You can make the web root its home directory if you want. If you don't need a home directory for a specific purpose then you don't have to create one. If you just created that user to make it the owner of /srv/www, then that should be enough if you don't require it to fulfill any other purpose. Home directories are useful when you need them, for example for users that will log in and use the system, or log in via ssh and need to be chrooted to their home directory (so they don't have access to other folders in the OS).