The whole sub targets is crap in my opinion. External weapons should get damaged much more easily than internal things behind armor.
I love the idea of it except ED have implemented it incredibly poorly. It doesn't even make any sense. If you're hitting these systems then you're breaching the hull aren't you - so what's going on inside the ships? In a universe where every single pilot targets the PP, why aren't the ship builders doing something about their ships to stop this?
The ridiculously simple mechanics in ED are to blame. There could have been more of a game to the scanners - you can't just target subsystems you have to use your scanner and find the subsystem on the ship first, none of this auto-crap that FD love so much (i.e. playing the game for you).
Then you could have the other ships pilot trying to stop you from scanning his ship and countering your scan. On a multicrew ship, this would be a lot easier as you would have a dedicated engineer, a dedicated pilot etc.
If everyone always targets the PP then it makes the rest of the ship pointless because you're not going to shoot at it. You might do for some variation because you're bored but really, if you're up against a competent foe you're going to target the PP every time.
So FD changed the mechanic so it doesn't kill the ship any longer - it just completely disables it.....
So we're still at exactly the same conclusion then - everyone targeting the PP only the ship doesn't blow up right away.