This would make combat so wonky and has no use, mechanically other than making you aim slightly more on one spot which you're already doing cause of how armor works in this game.
The only games that really pull this off are games like freespace. Because it's not about the weak point, it's disabling systems so that the ship you're targeting is less effective. Which is more defensive than offensive and not a requirement outside of specific objectives.
And part of the reason it works in that old game specifically is because it's about fighter combat and simulated scenarios, where disabling X on target and then defending it until it's captured/taken away is part of the overall plot/the whole scenario is designed around it.
It'd take away from the overall "fun" of this kind of game if you're "restricted" in a sense to shooting at the equivalent of a big glowing box on a giant enemy crab.
Targeting specific points on a thing as a mechanic is more sensible for something like arcade games or full 3d games where a lot of model itself shifts and/or moves.
It could make sense for specific enemy types in missions outside of the campaign where you could get a better damage output by firing into the big charging laser that opens up but again that's more part of the arcade aspect.
This is, as other people have said, not the game for it. If specifically because it's a strategy game more than it is a space flight sim or "side scroller".
Besides, AI issues or not would you rather Alex worked on a redundant, purely optional mechanic rather than the game the fractal softworks team wants to make. Time spent on things we don't need subtract from the things that are required/compliment what's already in the game/things that make the game more fun than something niche and extremely specific (and in my opinion a little weird. We have games like Axelay made in 1992 if you want to do this particular thing, other examples include r-type and major stryker. you know, one ship with a ridiculous arsenal vs many. See also: the bullet hell genre).
If anything this kind of thing belongs in a very specific challenge mode and all the feasibility aside, I think it'd just subtract from the overall game design if you had arbitrary weakpoints (other than places the shield doesn't cover, which is technically a version of this we already have).
Balance issues are probably my biggest concerns with this.
Freelancer is a good example of a game where this is technically -hidden power-.
Missiles and mines in freelancer, being the only explosive weapons, didn't account for some ships having more 'parts' than others. if you hit a ship straight in the middle with one, the amount of extra models attached to the basic frames like wings, would increase the hull damage taken. meaning a 1200 damage missile could teal uptowards 10,000 on the heaviest/clunkiest ship. which would more or less one-shot it. which the game probably wasn't intending you to do.
Hope that puts this into perspective for you.
