I think that should only apply to salvaged weapons, where the weapon is damaged (as it would be, you blew the ship to a molten husk, after all), so its performance won't be quite as good until you get it repaired.
So you get Mr. Tachyon Lance from an unlucky Paragon, let's say. Now, we all know the base stats of this beast, but when salvaged, it may be x,y or z% worse in whatever attribute until you get it fixed, just like with a salvaged ship.
Now, that's by no means a perfect system, but in my opinion, I think it's a good way to get some randomisation in with mass-produced ship equipment and makes sure that you aren't fielding inferior kit forever