If you can't change the USB compatibility from 3.0 to 2.0, that means the VM is either in "Powered On" or "Suspended" state. To be able to change the USB compatibility settings, the VM has to be powered off/shut down.
FWIW, I have an OmniKey 3121 USB card reader and it is recognised in a Windows 10 VM in Fusion 8.5.6 on macOS 10.12.5.
There are two modes for smart card readers in Fusion (and in Workstation as well), one is shared mode and the other passthrough. With the shared mode the card reader will appear as "Microsoft Usbccid Smartcard Reader (WUDF)" in Device Manager while in USB passthrough (i.e. as if the USB device is attached to the VM just like USB memory sticks) the card reader will appear as what your hardware ID is supposed to.
EDIT: Some smart card readers does not seem to work (i.e. it doesn't appear in the Connect list) if the shared mode is turned on.
You can turn off shared mode for the smart card reader by adding these two lines to the VM configuration file.
usb.generic.allowCCID = "TRUE"
usb.ccid.disable = "TRUE"