I assume you're looking at this part:
It says plain old missile, but I think it's lying I could be wrong, but I'm pretty sure that doesn't have anything to do with the ability's damage type. It's only determining the weapon effects. I assume the damage type is drawn from the only missile hardpoint in the PHASEBATTLESHIP.entity file, and that the damage type is described under damageEnum, and has nothing to do with effects:
I don't believe there's anything in the ability entity that determines anything about damagetype, and since there isn't a damageEnum in the buff entity either, my guess is it comes directly from the ship entity. Again, I could be wrong. I'm just pulling this all out of my ass.