Server 2012 deduplication: run on Hyper-V host or guest VM?
Deduplicating VHD and VHDX files is not supported. You should not dedupe on the Hyper-V host. Dedupe within the guest.
Edit: Note that this has changed a bit since this answer was originally written. In certain configurations relating to VDI, dedupe of VHD/VHDXs is supported: http://blogs.technet.com/b/filecab/archive/2013/07/31/deploying-data-deduplication-for-vdi-storage-in-windows-server-2012-r2.aspx