There are many cards (RBD, Lando, Dcaps, Walex, Montferrat, etc) that get discarded on use.

my question is this, if that ship is destroyed AFTER the card has been used, would the opponent get the points from that card as well, or just what was still on the ship?

Thanks in advance.

You always get the points for everything that was initially on the ship at the start of the game.

Page 13 of the RRG:

"If a ship’s upgrade card is discarded, it is flipped facedown but remains equipped for the purposes of scoring."