Qubes issue.
Not Whonix issue.
Qubes-Whonix isn’t different in this regard from a Debian based VM in Qubes. Qubes-Whonix has no special code that changes anything related to keyboard.
I haven’t seen anywhere that Qubes requires a USB keyboard to be connected to any specific VM. (Excluding USBVM.) Or keyboard support being VM specific.
There please contact Qubes support. See: