Here ist the NetApp KB article: SME unable to see database after Exchange Security update KB5001779 - NetApp Knowledge Base
For me it is not an option to uninstall critical security updates. However, Exchange Server 2016 is only supported up to CU11. Any newer CU is not supported and therefore I would not expect an solution by NetApp.
I have migrated to SnapCenter 4.4. (which was already runnig for SQL, VMWare and HANA). This is documented here
Please note that you can not restore an SnapManager Snapshot with SnapCenter.
Backup and restore works fine with SnapCenter and the Exchange Scurity updates.