This is a tough question to answer, and one I don't quite know the answer to. As the developer of Home Server SMART, the custom (home built) servers have always been the trickiest because of the wide assortment of disk controllers out there.
HSS uses the most common methods for accessing the SMART data, including some native Win32 functions and WMI. Many (maybe most) controllers support one or both of these, and thus I can get data without any trouble. I've always been able to get data from all of the drives on my EX487 and EX490, including off of the eSATA ports. Until last week...when I hooked up the Rosewill RSV enclosure and populated it with four disks. Then I couldn't get ANY data from any of the four disks! Interestingly, when I had just a single-bay enclosure, I could get data.
And then I upgraded the EX490 to WHS 2011 and installed the latest SiI 3531 driver, and I get information for all four drives!
Long story short, in most cases it is the device driver that exposes the SMART data, and in this case it was running a newer OS with a newer driver. No changes were required on my part to make Home Server SMART collect the data. So either the driver is making the data available through Win32, or through WMI.
I had a user send me a feedback via the bug report link that he could not get HSS to recognize the drives on his ASUS mobo in AHCI mode, but when reverting to IDE it did. Most folks will not notice a performance difference in IDE mode; the biggest gotcha is that if the system drive is attached to the controller, the server will blue screen--an OS rebuild is required. This is because the system uses a completely different device driver, necessitating reinstallation of the OS. So it's perfectly reasonable that HSS will recognize the disks in IDE mode.
You could also try a program called HD Sentinel (www.hdsentinel.com
) -- it's free for 30 days and is probably the best HD monitoring product out there. It can even recognize individual drives in many drive arrays!