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.
It's not semi-circular but rather "has a flat" and as already mentioned the indicated encoder is designed to be screw tightened on a shaft. So mechanically it should work provided the set screw has the appropriate depth limit required.
However, whether that means the encoder will work is undefined. The encoder pulse positions may not line up with the stepper angles as you desire.
Some adjustment of the encoder body angle to motor body angle may be required.