Can HEDS-5500 rotary encoder work with semicircular shaft?
The drawing for the encoder shows a hex wrench for tightening a set screw. That indicates it is intended to accept a flatted shaft like the one shown in the other link. The drawing for the HED-5500 encoder should show that more clearly and should show the diameter of the hole. Without knowing the diameter of the hole you can not determine if the motor shaft will fit.