Well I did a little app to test my thesis. 
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Unless I have seriously misunderstood how it work I fail to see how using a smaller gun is less advantageous or my app is doing something very wrong.
Your numerical results are largely consisted with mine. You present three scenarios, and I think that we can agree that in the first scenario with a base hitchance in excess of 100% the half-sized gaussguns have a definitve advantage (as both of us have argued earlier).
However I would like to draw attention to the second case. As I hope to have pointed out the most likely scenario is the missile salvo of 12, where the full sized gaussguns score 10.2 hits, while the half-sized ones score 9.8 (9.9 in my simulation, but nevermind). That is a 3.5% advantage for the full-sized gauss guns. Of course is not very large at all, but then again so is the benefit of a reduced gearing size on quad turrets compared to twin-turrets.
