De-dupe is at the volume level, so if you have mass redundancy in that 3TB, all in one is better for de-dupe. However, 3TB of files in a single volume presents problems for backup, and potentially DR.
If there is a lot of dedupe, you may want to use a volume snapmirror to replicate to any DR, because you get de-duped snapmirror transfers on VSM.
If you are doing NDMP backups, you need to have multiple qtrees at a minimum and backup at the qtree level. The more files to backup the longer and slower it will go, even with direct attached tape drives. Inodes are the biggest factor with NDMP backup from what I have seen.
Lastly think about where you are going to create your shares....trying to search through 6TB of files from a single volume level share would be problematic at best.