From this post I understand that you are doing NDMP backup of NetApp storage using Remote NDMP topology and also you have enabled deduplication.
You have dedupe enabled that means that data is travelling over LAN for sure. That means NBU is initiating the backup --> NetApp sending data to NBU server over LAN --> NBU receiving the data and processing single instancing (dedupe) and then saving the data in your dedupe pool MSDP/dedupe alliance.
But in all this excercise note that your data is travelling over LAN and NBU server is engaged doing all above mentioned tasks. If you wanna free your NBU server from these tasks then it is strongly recommended that go for Local NDMP backup topology. This will increase your backup throughput and redice your backup window. Also your major challange will be solved, as NDMP device itself will dump the data to target device over FC instead of it is sending data to NBU server for backup.
Hope this answers your query.