Missiles already have updates to their flight behavior planned, i mentioned that in one of these posts with you :p as for other weapon behavior, I do consider other options, for example, like i mentioned, power usage can easily be capped further to discourage further weapon size increases, the same could be said for power usage of the weapons. The thing is right now, defensive systems aren't even entirely implemented, IF we were to consider diminishing returns on larger weapons, it would not be until after those future systems are completed and various balancing options are considered.
Did I miss a post? Sorry I've been in a brain fever today going all crazy designing stuff and posting. Not enough coffee, I think.
Your post gave me an idea though - one way to create a tertiary effect to larger weapons that would make them a lot less useful against smaller ships would be to make them less accurate. Against a bigger ship, this is not so much of an issue but against a smaller one, it could be critical and frustrating - like swatting a fly with a sledgehammer.
You could also create a system whereby the actual firing reticle for larger weapons moves slower on the screen for fixed weapons - like trails the actual cursor, which would mimic gimbals moving slower.
Shit you could limit the range of motion for weapons as they get bigger too.
EDIT:
The more I think about it, just changing the behaviour of the firing reticle for larger weapons combined with mass on missiles solves a great part of the problem. That introduces a situational downside to larger weapons without making them mathematically less effective.
If it became difficult to hit smaller agile ships with big weapons, that would create a situation where the smaller ships gained an agility advantage which could be exploited by the right pilot. Defeating a quantitative advantage with a qualitative one through skill is some very gratifying emergent gameplay.