This seems to be a practice that Symantec is now promoting but there are certainly complications to this approach and cases where it simply won't work. "Ideally with dedupe" also depends on the data - we have a LOT of data that doesn't dedupe well at all and purchasing dedupe licenses would cost us a fortune with little to no gain.
If you have a NetApp filer and are using MultiStore, you now need to use multiple media servers to back up the same data since they are likely in different security domains. This could be further complicate itself by the way you have your physical backup network cabled - you may need to add even more network interfaces to separate the backup network from the production front-side traffic and figure out how to those media servers access the data over those networks.
Ff you have a NetApp filer (and there may be other NAS heads that have the same functionality) that have multiple security models on the same data, this approach simply will not work. We have some file systems that use both Unix and NTFS security so backing the data up using either CIFS or NFS will miss the rest of the security information.
No approach is perfect so you have to decide what is going to work best in your environment.
