The basic problem with them is thus:
With fairly high off type defense bonuses, where the square root value is equal or higher than the attack value of each INDIVIDUAL WEAPON, this problem is fairly clear. Basically, the drain to the defense after each shot is applied to the NORMAL value, not the square root... the result is that the square rooted value will only degrade by tiny amounts in the course of a round of battle. Each weapon is fired individually, which is the root of the problem, as weapons don't typically have high individual attack values until late in the tech tree.
To put it in numbers: if you were to attack a ship with 25 point defense using 10 plasma cannons (0-2 attack each), you would EXPECT that the 20 beam attack you have would allow you to overpower the off-type defenses with ease. This isn't the case. The first cannon would roll against a defense of 5. However, the defenses would not degrade properly... if the point defense had absorbed 2 damage, it would now have a base value of 23... meaning the square root is now 4, still a potent defense against a weapon that only does 0-2 damage! Even if EVERY plasma was absorbed by the defenses at full damage, it would take 5 hits before the base damage would drop below 16, making the square root defense 3... which is ITSELF a good defense against 2 beam attack.
Because of this, a defense that should have been like putting tissue paper in front of a bullet ends up taking little, if any, damage.
