If you want dedup you can't create a single drive on the NetApp which is >1tb because the maximum volume size for dedup is 1tb as you already know.
You can, however, map 4 or 5 LUNs to the windows machine and use Windows software based RAID0 (striping) to concatenate these disks into one.
Note however, that for doing that you need to convert the disks to dynamic disks, and using dynamic disks with SnapDrive is not really supported. It works though.
I did have some small problems in the past with such a setup, namely that when using Software iSCSI LUNs, the stripe volume would always show up as "offline" after a reboot, you had to set it "online" manually (probably some dependency problem between the dynamic disk driver and the iSCSI service). And you most certainly can't take any snapshots with SnapDrive on this volume because it spans multiple LUNs.
-Michael