When mine did this I thought it was actually topping out. It definitely wasn't bottoming out.
It seemed to me the clonk was when the wheel dropped off the other end of a speed bump rather than when I initially hit it.
When I put in Hagon progressive springs and oil it improved the handling but still clonked. Stronger linear springs and heavier oil might help. A GSXR front end definitely sorts it.
I don't remember being able to recreate the clonk on the sidestand though.