Will a 2012 mac mini i7 run parrallels?

Both will run Parallels. It all depends upon the performance you want.

16 GB of RAM may be limiting. It was limited when my 4-core 2013 Mac Pro only had 16 GB of memory and was running Windows and Linux virtual machines. In that case I use about 28 of the 32 GB memory I have installed now.

There's also Vmware Fusion, it does offer 3D services for improved windows performance.

I have run some pretty active 3D games and also autocad

I have run also run Windows 7 in fusion mining bitcoins on a 2009 Mac mini (4GB of RAM Core2duo 10.11) the mini was also a file, dns, & caching server.
No performance issues to report, the thing runs perfectly and quiet, no extreme CPU/GPU usage.

So, is there a performance hit?

Not much when doing 1 VM and 1 Host.
The CPU intensive tasks is where the balance must be found.

A mini could do it, but the 3D power is limited due to the small enclosure it has.

For that question I would answer, You don't need a Mac Pro. Why not consider an iMac instead of the Mini. An iMac outfitted similarly will be faster than a Mini, can handle more RAM, and comes with a Fusion Drive. The 27" top of the line 5K model is less than a Mac Pro and certainly faster than any other Mac model except for the Mac Pro. I'm quite happy with mine. Save a little and look for a refurb.

parallels is a virtual machine so it will not have direct access to the 3d features of the video card if the mac you look for has any

this will result in no fancy 3d gaming and no fancy 3d modelling programs

apart from that it will be sharing system memory and io with OS X so there would be a slow me down too

I run Parallels with Win7 on my 2012 Mini, I7 Quad 4, 16GB Ram and runs great.

The difference between a Mac Pro and a Mac Mini is like the difference between chicken salad and chicken poop. Does that tell you what you need to know?