Sure you can backup the shares in BE directly... But it's slow, terribly slow. You dont need to mount the shares like in NBU (which btw you notice they only talk about NFS) Which screws your Windows clients ;)
I cant stand NDMP and it's so restrictive.. But there isnt a better way to offer faster backups.
The best you can do is use all the ports in the NetApp if it has multiple ports, and just backup the CIFS shares over the network. 'Bout all you can do is get as much bandwidth out of it, as CIFS is terribly inefficient.
but NetApp Filer's should emulate CIFS shares in a Windows manner allowing share level backups - but themselves do not emulate Windows.
As I described in my private message to you to backup any NAS devices over shares the NAS device itself must either not have NDMP enabled or must have NDMP running on a different port from Backup Exec. You also must have at least one remote agent for Windows license installed on the Backup Exec Media Server - quick test for NDMP is try try using telnet on Port 10,000 to you device - if you get a response then this will make Backup Exec think that a remote agent is runnign when it isn't