Might have been some gameplay reasons that I'm now forgetting, too. Want to play devil's advocate and try to come up with some?
Having large shots plow through pilum swarms is essentially free PD. It makes missiles almost utterly worthless against ships packing large slots. The triple-HAG Onslaught design could probably even shrug off rocket swarms.
Having large shots miss missiles makes missiles much much more powerful against ships with large mounts. If you have enough missiles to overwhelm the PD, not that difficult to do if you go for it on purpose, then you can essentially cripple or kill them at will. E.g. the Onslaught has three forward-facing large mounts, which is alone more than all of its flux dissipation. At high flux it may be firing only those weapons. Conversely, if the AI is smart enough, a missile threat from the front could force the Onslaught to stop firing its large mounts, lest its PD get overwhelmed, which sounds like a win to me. On the Standard Onslaught, that means three HACs and two light dual ACs.
Yes, it's pretty hard to overwhelm two flaks using stock loadouts. However, fact is my PD gets overwhelmed sometimes, and doing it on purpose only means firing enough missiles at once or managing a coordinated strike from two ships at once. For example, imagine quad harpoon racks plus expanded magazines. Can two flaks stop 20 harpoons all at once? I doubt it. (...) Just tried it. My opponent Onslaught overloaded and lost almost half their hull. Red number 5700 right now...made it over 9000 before it turned enough to move the number, the new one's 1500, and it still hasn't finished overloading. Right, so there's that.
Oh right, bombing runs. Piranhas are already serious threats if you don't intentionally and specifically counter them. How much worse if the heavies can't hit the bombs? It would also make the fighters themselves die even faster, as the Onslaught's HAGs would be hitting them unimpeded.
Also, I would personally find everything but heavy mounts hitting missiles to be more counterintuitive and jarring, not less.
Is that all? Probably not. But enough for now.
That said I agree with Raynor. Missiles should weaken but not stop large shots. Though honestly this is mainly a problem for annihilators, which have enough ammo to stop, with luck, all such shots for an entire fight. Do something about annihilators and I would've thought it would stop being an issue. For example harpoons - one harpoon rack can stop one plasma volley. One harpoon pod can stop four plasma volleys, but the plasmas cycle slightly faster, and it means every harpoon did zero damage to armour.
It's only annihilators that can peel armour
and stop shots.