I might be totally wrong here, but I think the plasma and the rail gun don't get a damage malus when attacking bigger ships. Example, malus is 66% when a small ship with small hardpoints attacks an Anaconda, it will do less damage than against another small ship. So if you have 3 small ships with the same numerical hull and shield as one Anaconda, you still have to dish out 3 times the damage to the Anaconda. With rails and plasma, you would kill the 3 small ships and the Conda with the same number of attacks (incidentally, I think they also are the weapons with the highest damage in one hit?).
Or, in short: If you want to kill bigger ships, rails and plasmas are your weapons of choice.