Think of a SNAC as a plane dropped bomb, and imagine the mortar "shells" as a battleship long range fire, the plane dropped bomb is much smaller, but it has the advantage of hitting the target at angles of which the capital ship is not designed to be hit at, hitting weak sub systems, engines and so forth, and mortars tend to hit the front of the capship as they tend to face eachother while firing, say, two battleships could shoot at eachother for a long time at long range, but a bomber could come in and drop a bomb or torpedo and hit the battleship in a weak spot accurately. (not ingame bs, i mean say WW1 stuff).
this is the only remote logical explanation for the damage differences, sure a mortar can technialy score a "critical hit", but lets say it doesnt, just cause it cant be replicated in game.
thats all i could possibly use to explain to those that want realism.
perhaps a more realistic system would be to make Battleships patheticly slow, make SN's much much weaker, but make the Battleships weapons too slow to ever hope to hit anything smaller than a gunboat (low retfire) and low shield recharge, battles would last longer (especialy with bs vs bs), but people would say its boring, and so its fine as it is.