Just to close this out from my end, I had a faulty FC SFP on the Netapp connection, replaced it and the 0's for seconds at a time have gone away, all my drives are pumping at full speed now.
I am seeing a similar thing - I have a HP MSL4048 library with NDMP coming from a netapp 3240. Two drives are quick (110MB/sec) and two are slow at half that rate.
Looking at sysstat output on the netapp for the fast drives it is constantly writing...