how in the name of all that is holy am I supposed to destroy an entire fleet, then a boss submarine, with 52 missiles and 12 unguided bombs
As long as no landing ships reach the end of the battle zone before the first burst missile, you should be fine. Don't worry too hard about taking out every ship, since all non-objective ships can and will respawn.
IIRC, you should have available one plane with anti-sea missiles. Those will (should) take out anything less than a destroyer in one shot, and will obliterate all AA on everything but bosses. Use guns to take out the destroyers once their AA is gone. Drop a single missile at each heli, and use guns and missiles to take out the landing ships. As for the boss itself, focus on taking out its guns first - let your allies take the assorted aircraft that spawn from its launcher. If you're using a plane with UGBs, basically dump them in pairs on the sub's defenses - with any luck, you'll severely damage, if not destroy, a few of them. If you run out of all your main weapons, just gun it to death - if you're playing on Medium or lower, you have infinite gun ammo anyway.
Or you can just focus on the main part of the sub. Dealing enough damage to that section will send another TLS down from Arkbird, destroying any remaining defenses.
