It is not recommended to do NDMP Option backups of VMware VMs held in datastores on NetApps as you get zero GRT capability and it would mean that the smallest container object that could be restored would be the LUN that holds the datastore. In practice this would mean if you want to restore one VM (or one file from inside a VM) from a few weeks ago, all the VMs in the LUN would have to be restored from that same date.
This means that the SAN transport method that is part of the VMware (Virtual Machine) Agent is the recommended method to backup the VMs when they are stored on an NDMP option device (as long as you can connect the LUN to the Backup Exec Server as well as the ESX host)
More details on the various scenarios here: https://www.veritas.com/community/blogs/lan-free-including-san-backup-configurations-with-backup-exec
With regards the replication that you also mentioned:
If the replication does not touch either CBT against each VM or VSS inside the VMs themselves (so makes zero quiesce calls through the VMware tools) then you may be OK. However if it touches CBT or makes quiesce requests then Backup Exec will have issues with Incremental Virtual Agent backups and may also have problems identifyng the unused space within the VDDK files. I also don't think we officially test such a configuration which would mean limited support based on our definition of Alternative Configurations (which can be found in the SCL and HCL documentation). Kind of means it would be down to you to test the backups and restores and confirm no issues.
As an aside we don't officially test NDMP option backups with the type of replication configuration you ask about either.
