This would be better described as
The AI currently does not take into account target point sefense when launching missiles.
Guys, it's far worse than that.
It's quite aggravating when half my fleet dumps all of their harpoons on a single Hound that appears at the beginning of a fight, but I've actually seen ships spam harpoons... at overloaded fighters and bombers.
Wut.
Wait, seriously? they throw harpoons at fighters?
*Snerk*
I think there are several factors that need to be taken into account.
Point defense in area. (Take into account flux levels of ships in area. Splash variants are more notable)
Allied support (allied fighters or missile launchers to eat up some point defense.)
Value of target (Don't use harpoons on fighters)
Vulnability of target (overloaded/flameout. Prioritize targets you can hit effectively.)
How many other missiles are already being used (Don't throw another harpoon vs a hound if 3 are already on their way.)
Its a complex problem. Just stating these 5 factors makes it clear that a quick if/then/else tree isn't enough. Not surprised the current algorithm has issues.