Ships don't really have enough hull for that to matter and generally once you're shooting at hull things like DPS and OP efficiency don't really matter because ships are disabled. The tough part is punching through armor and shields and well... there isn't much reason to have a Thumper instead of another Heavy Mortar
The reason is speed. Thumper can hit more easily when Arbalest and Heavy Mortar alone can miss due to slow, somewhat inaccurate, and synchronized attacks.
Generally, I would use two Arbalests and one Heavy Mortar (when I cannot use two HVDs and one Heavy Mauler). Occasionally, I use Arbalest, Heavy Mortar, and Thumper.
People tend to think that unarmored ship equals dead. I do not always agree with that. Ship is disabled when it is disabled, not as soon as it lost armor, if there is nothing ready to finish it off as soon as armor is lost.
Heavy Mortar is a shockingly effective weapon against sub-capital armor if you can hit the target (which can be hard due to its slow velocity - ordinance expertise 1 is really good for it). Good DPS, good efficiency, very low OP costs, and the per shot damage is still ok. For long range work the Heavy Mauler is better, but if you want to be closer it is a superior weapon.
Its not the best ballistic weapon (I'd vote railgun), it is imo the most under-rated weapon.
Heavy Mortar is the only medium option if player does not have enough Heavy Maulers. I use Heavy Mortars all the time because they are one of the few weapons that are common, and one of the fewer still that are relatively effective (like Hellbore and Mark IX).
I would call Arbalest more under-rated. Yes, there are better alternatives, but Arbalest is very common, unlike Railgun, and effective enough. I use it when I only have Heavy Mortar for HE because the ranges match. Sometimes, I use Arbalests when I have rarer weapons available because I do not want to reload a game as soon as I lose a ship with Railguns, Needlers, or HVDs on it, and weapons are lost forever.