Aha, I missed that part, sorry! Read it as being 400 per shot, not total.
Are you 100% sure the per-shot damage is indeed 20? Also, might be worth testing in an as-vanilla-as-possible to try to narrow down what might be going on.
... in other words, no, it doesn't make sense, and I can't see how that would happen either. Although it's certainly possible if say the damage-dealt or damage-received stats of the ship/target are modified by something else.
OK, I
might have figured it out, but this is mostly speculation:
The problem
does not persist when I ceased spawning the projectiles via scripted means [sorry I didn't mention that first, btw: might have explained a lot]. However, the behaviour of the scripted projectiles is completely fine as long as it doesn't impact hull/armor: shields work just as intended.
Thus, I believe the issue is that
setting a projectile's damage via script only changes the impact damage, and not the AoE damage from a flak projectile. I might be completely wrong, but that would explain a lot of the behaviour, since the Fuse-based detonations might not affect shields in the same way as hull.