I have a big missile boat that has a ton of harpoons + missile racks, but the AI does not fire any missiles.
I'd like for the AI to launch all missiles at one ship (focus-fire). How can I get the AI to do that?
Easy.
Overload the enemy ship. If there's one thing the AI is good at, it's absolutely unloading Harpoons at an overloaded or even just high-flux target and obliterating the thing.
Also, how can I get the AI to fire only enough missiles to actually destroy a ship and get through shields, but not waste too much ammo?
In stark contrast to the above (and perhaps because of the above behaviour) this isn't really possible. The AI has some tags and procedures for conserving ammo, but it conserves ammo only to unload at opportune moments. I don't think there's a way to tell the AI
not to unload at such moments.
Out of interest, what is this "big missile boat"? What's the hull, what have you armed it with overall? (A screenshot of the refit screen would be nice and concise here)