The info on Shoemaker 9 I saw on The Science Channel, if they’re correct in what they said. What sources were you looking at? Face it, without big brother Jupiter out there it’s likely we wouldn’t be here. However the Big Guy can’t catch them all and one day it’s going to be POW!, Goodnight Irene! If the cratering of the Moon didn’t all occur in it’s formation then when did the rest of it? And when has the Moon ever acted as a cosmic shortstop, I’m curious to know? Mercury shows evidence of heavy bombardment as well as Jupiter’s moons Ganymede and Callisto. Because Europa’s surface, if not the entire moon itself is one big ice ball, it’s surface shows less evidence of cratering but only because the surface keeps freezing and then cracking apart.
http://en.wikipedia.org/wiki/Comet_Shoemaker%E2%80%93Levy_9
Prior to that, it was most likely orbiting (basically) between Mars and Jupiter:
Benner, L.A.; McKinnon, W. B. (March 1994). “Pre-Impact Orbital Evolution of P/Shoemaker–Levy 9”. Abstracts of the 25th Lunar and Planetary Science Conference, held in Houston, TX, March 14–18, 1994 25: 93.
(Reference 8 in the Wikipedia article.)
http://adsabs.harvard.edu/abs/1994LPI....25...93B
Also see references 39 and 40 regarding Jupiter's role as a “cosmic vacuum cleaner” (it's unclear, as Jupiter seems to help with regard to asteroids but may make comet impacts with Earth more numerous.)
The Science Channel gets lots of things wrong...
It is also worth noting that perturbations from Jupiter are the main reason the mass of the asteroids did not accrete into a larger body, but instead was broken up into smaller bodies, some of which end up coming our way.
Now as for the cratering of the Moon, MOST of it occurred over 2 billion years ago, but impacts have most certainly continued at a slower pace, as they have on Earth. For example, Tycho (a truly spectacular crater) is believed to be only about 108 million years old.
http://en.wikipedia.org/wiki/Tycho_(crater)
and
http://www.imageagain.com/Strata/StratigraphyCraters.2.0.htm
Last, where did I say the Moon had acted as a cosmic shortstop? It's gravity well is clearly not big enough to do so consistently. That weak gravity is in fact a major reason why (eventually) it would be a good place to launch an asteroid interceptor or interceptors from.