Well you can't dedupe an NDMP stream with BackupExec.
The best performance is when you are doing NDMP over FC to tape directly.
The granularity of restore will be down at the volume level or file level if DAR is enabled.
If you backup over NDMP you have to restore over NDMP so in the event of a disaster you will need another EMC device.
Also if you have mounted LUNs stored on the EMC device but attached as volumes to Windows servers, then assuming that EMC LUNs work like NetApp ones then an NDMP backup will see the LUN as a single file with no granularity inside it. To backup/restore the individual files inside the LUN you would have to use an agent for windows installed on the server that uses the LUN and not use the NDMP option.
If you jave just used the EMC device to provide CIFS shares then you will have individual file restore capability within an NDMP backup.
Currently I'm encounter this issue.
Adding EMC VNX 5300 Filer to Backup Exec fails with an error "The requested operation is not supported"
Please see the linke below