When talking about NDMP and datadomain there are some trade-offs. First an NDMP stream doesn't de-dupe as well as an NFS or SMB backup stream. So there's that. Second, when backing up a dataset with NDMP, in most cases you cannot restore it via NDMP to another vendor's system. I see this pretty often with customers who have moved from NetApp to Isilon, and have backup tapes with NDMP streams from NetApp, but cannot restore that data on Isilon.
Besides that there certainly are customers using EMC Networker with DD Boost, and writing to Data Domain the NDMP Streams.
Mounting via NFS and backing up that way is an option, but to be frank, only one I would consider as a last resort. The reason is pretty simple. Permissions. When backing up over NFS, you're only going to get POSIX permissions, which most likely don't reflect the true composition of the security structure. So when you perform a restore, yes you can do redirected restores, but you've lost some of the metadata associated with that file. And yes, most customers when they get to a certain cluster size, say 500TB-1PB stop backing up their clusters, or at least they stop backing up the entire cluster. Instead they backup critical data sets, like EDI applications, or other business critical apps, and SyncIQ everything else.
The other thing that can help here is a full once, incremental forever strategy.
Hope this helps.
Senior Solution Architect
EMC Isilon Offer & Enabelment Team