I did some searching and couldn't find a definitive (to my tastes at least) answer to whether or not Moff Jerjerrod cancels one of the hits on a Direct Hit critical card. Can he be used to cancel the "effect" of a Direct Hit critical card (making the card count as one point of hull damage), or is an "effect" limited to Pilot and Ship critical cards?

Yes. He flips the card facedown without resolving the card's effect. This means it is simply a single hull point of damage.

And FYI, the direct hit damage card is a "ship" damage card so any effects that only target "ship" cards will work against it.

The text on Direct Hit causing it to count as 2 damage only applies when it's face up.

When you get a Direct Hit, it should normally be left face up and it counts as 2 damage cards if so. DO NOT, as many people do, flip it down and draw another face down card. That's not what it says to do, and there are many game efefcts which can flip either or both cards face up and mess the whole system up if you do.

The fact there is an effect or not to resolve is irrelevant, you flip the card down and you don't resolve its effect (If there is one) The card do not say "If there is an effect to resolve, flip the card face down and do not resolve it."

If I tell you: "go to your room, don't pass by the kitchen and don't take a drink." The fact that you may not want a drink in the first place does not give you the right to not execute the rest of my sentence...