Q. Can I use the Windows Server 2012 Data Deduplication feature on my Exchange, SQL Server, or other databases?
A: Is what you want to do supported and is what you want to do possible? Typical questions, but for this specific question the ultimate answer is the same.
First is the issue of support. To use the data deduplication feature on a workload, you need to ensure that there's product team support deduplication at the file system level. At this time, teams like Exchange and SQL Server do not support this, for the next reason (among others).
Second are the technical possibilities. Data deduplication works at a block level on the file system for any type of file. However, if a file is open by a process with an exclusive open, and is locked when the deduplication process attempts to optimize the file, then it's skipped. Services such as Exchange, SQL Server, and Hyper-V keep their files exclusively locked, which means Windows deduplication wouldn't deduplicate those files.