Ok 1 is easy, you can *always* choose any option on a 'choice' crisis, and generally make any choice *unless* there is text sayign you cant. Hence crisis cards that say *discard X cards* become easy options if the affected player has no cards as there is no penalty.
Exceptions where the choice *is* restricted I believe are limited to
-"build cylon detector" where it specifically states "you cannot choose this option if you have no nuke token to discard"
-Mutiny cards where they have bold text printed on saying things like "you cannot play this card if you have fewer than X cards in your hand", "you cannot play this card if you are the president" etc etc
-Do not the errata note in the official FAQ on the FFG website affecting the "unwelcome faces" skill card (they printed 'may' where it should read 'must'
2. They skipped it on the quorum card 'presidential pardon' too, we have an answer somewhere that presidential pardon is intended to be discarded on use, I'd expect the same 'discard' applies to this one too (it's not strong enough to be a 'remove from game' one -esp as the blue 'raptor specialist' card comes around multiple times in the engineering deck)
3. this card has been acknowledged as an FFG screw up, it should be treated as 'discard all nukes' not remove them from the game. All other remove from game effects are as you describe, put them away and never use them again.