It might be that I have the wrong idea about Nethserver, but to me Nethserver is oriented towards providing network services like DNS, DHCP, AD DC, SNMP, mail, etc. Nethserver isn't oriented towards providing large amounts of storage, as indicated by the fixed location of the shared folders on the boot drive and the lack of any kind of way to deal with storage mediums. When you need any reasonable amount of storage via shared folders or use the Samba users home folders it needs to be stored elsewhere, not on the boot drive. Be it a separate drive in the server or some form of network storage. For network storage the backup isn't Nethservers problem to fix, if the storage is on the server there are probably some simple ways to automatically update the needed backup paths.
In my case I'm trying to get Nethserver/Samba to handle a Ceph storage cluster. So either via Samba VFS or mount the CephFS in Nethserver and then a normal Samba shared folder.