Actually my technical reasons for preferring size-6 were considerably stronger in previous versions of the game, and from C# 2.0 (or 2.2?) onward there are strong arguments for using larger missiles.
There are, of course, still strong points against them. More conspicuous, both on RADAR and on Thermal. Slower reload. More limited number of missile tubes. Fewer missiles stored in the magazine.
But the new "bells and whistles" of Active Terminal Guidance, Missile ECM and ECCM, Retargeting capability etc all argue for larger missiles, as do the new "shock" rules from massive impacts.