5. Therefore, upgrade cards that affect pilot skill would still be in effect, since they are a) still attached to the destroyed ship and b) not technically affecting a ship in play, but the destroyed ship.
This is a huge assumption, though. The simplest rule would be "When a card has been removed from play, it has no effect." You're positing a rule instead that "When a card has been removed from play, it can only affect other cards that have been removed from play."
So why introduce that additional complication? The only thing it changes at the moment (that is, barring additional references to destroyed ships) is the VI - Nashtah Pup interaction.
Once the cards are off the board, I don't think it matters what type of card they are, they cease having an effect on the game. The way I see it you've got an all or nothing situation depending on whether the stats for the Pup are something that are set at the time of deployment or if they are evaluated constantly.
If the Pup gets the PS and ability of the Hound's Tooth at the time of deployment (which is what I tend to believe) then the stats of the Pup are affected by VI, Damaged Cockpit, Injured Pilot, Swarm Tactics, Decoy (and maybe a couple of things that I forgot).
If the stats for the Pup are not set at the time of deployment but are more or less just variable that are linked to the VY-666 pilot card then neither VI, Damaged Cockpit, or anything else is going to continue having an effect.
