I think the answer is much more trivial. Each hit that takes HP also inflicts Fatal Wounds. It doesn't take much HP loss to inflict Fatal Wounds; I think 9 damage is the minimum required for 3 Fatal Wounds per hit, and you can't take more than 3 Fatal Wounds per hit, no matter how strong.
Now, Stun damage is, afaik, only inflicted when Fatal Wounds are inflicted (or at leas most of the stun damage is generated that way).
So - shotguns inflict relatively low HP damage, but due to multiple hits, they're prone to inflicting many Fatal Wounds (and, therefore, high Stun damage).