Acronis Files Connect (formerly ExtremeZ-IP) uses alternate data streams (ADS) for storing Mac specific data (resource forks). As it happens, Windows Server Deduplication will only dedup the primary data stream of a file, an ADS will not be deduped (see the linked Technet article, below). This may limit the benefits for files that are accessed from the Macs. It is also important to understand that in the OS X 10.7 and higher SMB client, Apple uses the same ADS formatting that is used by AFP with Acronis Files Connect. In this respect there is no better alternative that is native to the Mac.
While it is true we have not tested this feature of Windows Server and do not officially support it, we are not aware of any issues.