CIFS is a protocol used to access shares, typically CIFS shares are not used to expose volume root or system folders and are only usually used for user data folders. As an aside you do still need a Backup Exec remote agent license to do CIFS backups
NDMP is a protocol that is usually used to access data (usually for backup purposes) on NDMP compatible devices. It does not do the access via shares but does it via application calls (APIs) directly into processes running on the NAS device. Typically the NDMP protocol can access the full structure of volumes present in such devices. Again for BE a specific license is needed but then you can choose to attach a library to the back of the supported NAS device or to somethign on the media server.
CIFS and NDMP are separate, an NDMP compatible device can host CIFS shares which means that data in the share can either be accessed at Share level (via CIFS) or at device/volume level (via NDMP)
As a similar scenario think of this:
Windows server running ftp services. There is a folder on one of the windows volumes that is also the ftp store. This folder is also directly shared via Windows sharing (in effect CIFS) This data in this folder is accesible in 3 ways - but ONLY one of the ways can get to the volume root (ftp, windows sharing or direct file system access at either local user or local service level) Yes in the windows world the volume root has a hidden, admin share on it which is similar to what I have already told you about your question.
You have not explained why you need to backup these folders, as most NAS vendors have a quick way of recovering their operating systems typically you would not need to back these locations up, just keep a document handy that provides you with any specific configuration information.
