They also don't seem to follow the damage = Mk I damage * Ship Mk formula.
I looked but couldn't find an example. The Heavy Beam Cannon hasn't followed that rule since basically ever (and the flak actually gains more secondary targets at higher marks, thus being more-than-linear), but is there another one you're seeing that doesn't?
All damage numbers are Normal combat style--not sure if that helps, or if that is imply informative for you.
Basic III: current damage: 97,600 x3; expected damage: 97,200 x3 (32,400 * 3)
MLRS III: current damage: 17,120 x12; expected damage: 17,040 x12 (5,680 * 3)
Missile III: current damage: 132,000 x3; expected damage: 132,000 x3 (44,000 * 3)
Laser II: current damage: 24,400 x3; expected damage: 24,480 x3 (12,240 * 2)
Laser III: current damage: 36,400 x3; expected damage: 37,620 x3 (12,240 * 3)
Lightning III: current damage: 9,760; expected damage: 9,720 (3,240 * 3)
Flak II: current damage: 81,600; expected damage: 97,600 (48,800 * 2)
Flak III: current damage: 104,000; expected damage: 146,400 (48,800 * 3)
*I understand that Flak and Lightning could be affected by their "area" damage. I only include them for completeness. HBCs, of course, are a completely different animal, and are not included in this list.