These are links and have to be links and not files. The owner of the link shall be root and the permissions are fine as well.
Further investigations show that in the folder /etc/nginx/sites-enabled/ on server1 are not the same with server2 do i also have to sync them just as the /var/www/ folder?
No, they are synced by ispconfig. Dont apply any other sync like unison on them or you will break the server!
If they dont get mirrored by ispconfig, then your slave server is not setup correctly or you did not add the salve server before you added the first website on the master. The most likely reason is that the slave can not connect to the master due to wrong host settings. See here for debug instructions:
Reagrding the unison sync problem, if your slave server is not connected correctly to the master or you added sites on the master before you added the slave, then the users that own the files dont exist on the slave which will explain why unison has to store the files as root.