Wow. This discussion could give "Who's On First?" a run for its money
Here's the full scoop, all at once, to hopefully clear up any remaining confusion:
Normally, uncanceled attack dice results turn into damage.
Damage is resolved one at a time. For each damage:
--- If the target has a shield token, it loses a shield.
--- If it does not, it is dealt a damage card
------ For standard damage, that card is face down
------ For critical damage, that card is dealt face up
Sadly, "damage" is also a term which is used for how many hits your ship has taken. That's the "damage" which the Direct Hit card is referring to.
The Proton Bomb skips damage completely, and just deals a face-up card. That's why it ignores shields - because it doesn't deal damage.
The Direct Hit! card doesn't ignore shields, because it can't itself ignore shields, because it has nothing to do with shields.
Hopefully that covers everything