I've been experimenting with Windows Server deduplication on the disk used for SmarterMail storage for several months now.
From what I could see, everything works fine and saves a lot of space!
In my case, it went from 1.9TB of occupied disk space without deduplication to about 1000GB with deduplication on.
Almost half!!!
Gabriele Maoret - Head of SysAdmins at SERSIS
Currently manages 6 SmarterMail installations (1 in the cloud for SERSIS which provides services to a few hundred third-party email domains + 5 on-premise for customers who prefer to have their mail server in-house)