its a weapon skill, it ahs a chance of taking the sub sustem offline, tends to be a phaser skill.
so if I hit a ship and it triggers 'Shields System offline' you will see the shields on the enemy either los the bank I have hit or the entire system will go down, it only lasts for a few seconds. the higher you phaser skills the more chance you have of doing it, but it is only something like a 0.5% chance
if you hit the weapons, the enemy will lose that weapon, or all the weapons will become super weak (like if you went from 100/100 to 0/100)
you will find it happen to you once you get upto level 25ish, you will find a wepon system grayed out and cooling down very slowly, basically enemy hit your weapon subsystem, only way to get it back online is to use 'Emergeny Power to XXX' to repair the affected system, or it auto repairs once combat is finished
No idea if it perm takes down an enemies weapon, but I have seen them lose their beam weapons during a fight