Here's the problem: for most races, the long range frigate is the first military frigate you CAN research (next to siege, which is not useful in combat). To have THAT counter something much further down the line (support) is pointless. It needs to counter the main unit type or else the research would be wasted in any fast paced game. Also, look at what else you have. You have specialized anti-fighter units, which are good against large groups of units, but from your "realistic" point of view I don't see them countering light combat frigates either--their ordinance will be optimized with a view to killing small, fast, lightly armored craft, and clearly the light combat frigates don't fit that description (just compare them visually to strikecraft). Then the next thing you have is carriers, so basically if LRM didn't counter light combat, you'd have to tech to carriers with fighters to counter them. This would make investing in research a very risky proposal.
To me it does make sense that long range counters light combat, even realistically. Light combat frigates are, as you say, agile and fast, with medium to low damage output. They might have been invented to fight off similar vessels or maybe even rebels in combat retrofitted trade vessels. Clearly they have a role lateron in quickly engaging support vessels as well. Once you get to LRMs, though, you have smaller, even more fragile vessels with a large damage output. If Sins was a much quicker game it would make sense for LRMs to destroy light combat at range and then be destroyed by them if they ever catch up (kind of like archers vs grunts in war3), but that's not the kind of game sins is. In Sins, combat does become somewhat static at a point, and so the decision was to either have lrm counter light combat or not. I think they made the right decision from a game balance point of view, and I can buy the decision from a realism point of view.
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