Windows Server 2012 (or 2008) on a Mac mini I understand Windows Server 2008 (and presumably 2012) works with Boot Camp. But I am wondering if it will be able to access the second hard disk in the Mac mini server.

Can a Boot Camp Windows use the second hard disk as a NTFS volume?
Yes it can. But it would be better if you first format the disk in OS X as any type you wish, then format it in Windows as NTFS.