Beams are in general intended for support roles, as they have efficient flux costs (effective cost = cost per second - flux dissipation per second), long range and instant hits, while dealing less damage against armor (they deal half damage, in case of Longinus, it's equal to a projectile dealing 375 damage per second) and deal soft flux against shields. Burst beams are also falls into support category, but they are a bit more effective against armor as their damage is calculated by the burst's damage per second. As they are support weapons, they are generally dealing energy damage - jack of all trades but master of none.
Now, if you change the damage type of Longinus into HE, they will be rather ineffective against shields indeed, but they will deal HUGE amounts of damage to armor. It is already balanced as it is, cost/damage wise it is not efficient (save for the templar ships) and a ship with 0.5 flux/damage won't build any flux by having 375 flux dissipation for each beam - meaning that it will cost more to the source ship (even to the templars).