Simple Question:. Does your ship have to have 3 damage cards on it to use RBD, or can you discard it to remove one or two?

You certainly can.

Quote

At the start of the Ship Phase, you may discard this card to discard up to 3 of your facedown damage cards.

Without the "up to" you would have to discard 3.

But there is no word that the ship need 3 damage cards, and that you have to choose exactly 3. You can choose 0, 1, 2 or 3. And even activate it while you have 3 or less cards on the ship.