Data deduplication in Windows Server 2012 is a nice feature, but one thing it cannot do is deduplicate running virtual machines. That limitation is removed in Windows Server 2012 R2, albeit specifically for VDI (Virtual Desktop Infrastructure) deployments on SMB 3.0.
That being said, this new capability could greatly increase the overall effectiveness of deduplication for VDI implementations. As a side benefit, deduplication greatly improves boot performance of virtual desktops.
In addition to storing the VMs on SMB 3.0 (required), Microsoft highly recommends using Scale-Out File Server on Windows Server 2012 or Windows Server 2012 R2. Cluster Shared Volumes are supported for high availability.