This is based on my experience with VSC 4.2.2, but I guess it still applies.
VSC's job is to trigger a NetApp volume snapshot, so it will actually backup any data that belongs to that volume, presumably a (full) VMware VMFS.
If for any reason you want to selectively keep backups of a single VM or vmdk, you'll need to move it to a new VMFS, in its own NetApp volume.