I know this is an old thread, but has the OP had any issues with having the iTunes library on a Thunderbolt drive? I have been having issues with a CalDigit T3 in the same situation upon waking from sleep. If I never let the Mini or drives sleep the everything is fine, but if the Mini and/or drives go to sleep and I try to connect to the shared library from my AppleTV, the AppleTV will sometimes time out while trying to connect. I never have this issue using an external G-Drive (USB2) or WD MyBook (USB3). I have tried both using the software RAID setting and JBOD setting with the same results; It takes my AppleTV about 10-15s to connect using the WD and 45-70s to connect using the T3. The only conclusion that I have been able to draw from all of this is that Thunderbolt does not work as a connection for your iTunes library.
I also tried putting my home folder on the T3 initially but the Mini's GUI was completely unresponsive for several seconds upon waking, so I had to move the home folder back internal.