Yes you can, but you will get absolutely no dedupe. Only NetBackup can dedupe NDMP, and it's only NetApp at the moment. BE is about 12 months out from getting that.
You can backup user defined shares to the dedupe store, and do media server dedupe. That is a viable workaround. Though depending on how much data you have, you will want to trunk multiple links on the filer and BE server to get more throughput to make sure that you can fit everything in your backup window
