Counter-design is terrible. Don't do it.

If bombs need fixing, FIX BOMBS.

(also, poor punisher )

As someone who both loathes the current state of bombing, but loves ordnance and ordnance carriers, I'm not super crazy about this. Conceptually, and thematically, I'm all about it. Aiming for the magazine has been a traditional way of disabling heavy weapons units and pieces since their conception. In this game, however, the idea of detonating the entire arsenal of ordnance is... a bit too far. Citruscannon's version is a bit more restrained, which I like, but technically bombs aren't an attack, so it would only effect other missiles/torpedoes in it's current wording. It also doesn't stop someone from simply discarding a munitions token instead of the actual card (following the Boba Fett ruling).

Also, despite being unique, it can still be abused. Being unique wouldn't prevent it from having an Extra Munitions token, which would considerably change the potential of such a card. The upcoming reload action would also have something to say about how much use you could pull from it; it's not something you'd stick on a Gunboat, but the Kimogila could put it to enough use to literally kill an archetype (albeit one I wouldn't be sad about seeing the back of). Even without reload, a Scum carrier with Scavenger Crane could easily get multiple uses out of it.

Lastly, as was mentioned previously, it's a silver bullet to a specific archetype. If that archetype (namely the bomb-heavy lists) goes away, so does the card. Alpha strike lists aren't common enough to warrant pushing 5 points into insurance, especially when the nature of alpha strike lists means ditching one missile card likely won't make a dent in the single round firepower of that list. Similarly, TLT lists would usually be more efficient in simply destroying the carrier quickly than discarding the card.

As I said, I like the idea, but I think the approach is almost there. If you want to make this a missile (because a little fluff won't hurt sometimes), you probably need to make it 4-attack, and give the option to cancel all dice on a hit, or use the initial damage roll.

Personally, I like the idea of using the missile to assign a condition card on a hit. The condition card could be assigned to a secondary weapon of your choice, denying use of that particular weapon regardless of the number of munitions tokens stacked on it. This increases it's effectiveness against token stacked ordnance lists (where it would have been lacking), maintains effectiveness against Bomblet Generator and turret/cannon secondaries, but it crucially prevents abuse of multiple uses by only allowing the condition card to effect one card on one ship at a time.
In this orientation, I think the missile damage should stand at whatever was rolled, with the modifier that a die set to a crit facing is added to the attack, rather than cancelling and re-rolling for whatever ordnance is on board the target. This clears up any issues with ordnance that doesn't roll for damage, or doesn't meet the "perform an attack" qualifier. It also means it's not useless in a game where nobody has any secondary weapons (which is fairly unusual these days).

tl;dr this is just my two cent on it. Conceptually and thematically I love it, but I'm not super into that iteration due to potential multi-shot abuses, and high specialisation.