I think the main reason is that Pluto has an active atmosphere; it snows. Plutos icy surface may be somewhat active as well, so craters may disappear over time in a way that the craters on the moon cannot.
However, there may be other factors:
1. As you note, the mass of the Earth-Moon system is much greater than the mass of the Pluto-Charon system.
2. In the Earth-Moon system, the moon is the outer protector. In the Pluto system, there are five smaller protectors and Pluto is the protected.
3. The inner solar system is a small, dense region closer to the gravity of the sun and gas giants. Objects thrown in our direction are likely to stick around. In contrast, the Kuiper Belt isn't very dense and objects thrown in that direction not only have more places to go, but may be on their way out of the solar system or into extended hyperbolic orbits.
3. KBOs aren't very dense, so even impacts which occur may not create massive craters.
However, there may be other factors:
1. As you note, the mass of the Earth-Moon system is much greater than the mass of the Pluto-Charon system.
2. In the Earth-Moon system, the moon is the outer protector. In the Pluto system, there are five smaller protectors and Pluto is the protected.
3. The inner solar system is a small, dense region closer to the gravity of the sun and gas giants. Objects thrown in our direction are likely to stick around. In contrast, the Kuiper Belt isn't very dense and objects thrown in that direction not only have more places to go, but may be on their way out of the solar system or into extended hyperbolic orbits.
3. KBOs aren't very dense, so even impacts which occur may not create massive craters.