Actually, both Kick Hopper and Punch Hopper had a clock up. It was explained in the Masked Rider System Photobook that they had the ability to do so, plus in the PS2 game they show as having clock up.
The trick to the fight is, can shotaro separate the hoppers from each other. The two hoppers need each other, because they are essential incomplete versions of the Bee, in the terms of style. If shotaro can do this, then he can win. But if, and thats a big IF, the hoppers did clock up, all they needed to do is remove the memory from the slot.