Jeff,
I've been using Scanner on both a WS2008R2 host and Hyper-V guest WHS2011 since last Fall with good performance. (You can probably still get a bargain discount for an additional Scanner license.) However, Scanner would have to work on your host, and Drashna indicated it might not on Hyper-V Server 2012. You should be able to test it yourself in trial mode on the Hyper-V core.
On the host, Scanner reads temperature and SMART data from all the drives, even the ones that are offline and being passed through to the VM.
Here's what Alex told me in a support contact on coordinating Scanner use in both the host and a guest last October, which I've been doing:
"If you don't have SMART data (such as when using Hyper-V), the Scanner can only warn you at the first sign of data loss, in order to prevent further data loss. If you have SMART data, then Scanner will monitor the various counts of sector reassignment and will let you know of any potential developing issues. But this is not possible when using Hyper-V as I will explain later.
"Hyper-V virtualizes the disk controller. In other words, all commands that get sent to the drive have to go through this virtual controller. When I last tested it, the virtual controller refused to forward any kind of SMART commands to the drive. Because of this there is really nothing that Scanner can do to get SMART through these virtual controllers. Microsoft has to implement SMART support, there is really no other way.
"If you want to run Scanner on both the Host and Guest, in order to take advantage of file evacuation, I would suggest you do it like this:
Turn off Start / stop automatically on the Host. This will prevent surface scans from starting, while still monitoring SMART. Install Scanner 2.2 and DrivePool 1.2 on the guests with the default settings. The default settings will perform surface scans and will evacuate files when damage is detected. The only thing that you won't be able to get working is file evacuation on SMART warnings. But this is not enabled by default, so I don't think this is a big loss."