That's strange. With Windows Server 2012 R2 you shouldn't have to import the module if the installer put everything in the right place.
At any rate, now that you've upgraded to clustered Data ONTAP 8.2 or newer, you can take advantage of Windwos Server 2012's native copy offload feature called ODX. This will usually offer similar performance to the Copy-NcHostFile Cmdlet.
Give it a shot, and let us know how it works for you.