The Mac mini does well with Windows. Some of our customers will run Boot Camp in order to boot Windows directly. But, the more popular choice is to run Windows as a virtual machine using an application like Parallels.
When you run it as a virtual machine, keep in mind that the two operating systems will share the available RAM. So, it’s advised to have the full 16GB of RAM for peak performance.
Many people prefer the virtual machine because OS X would be the main OS. It seems to do better with remote reboots and coming back on it’s own. Then, you have the Windows install to work on within that canvas.