Its most likely shield mitigation. Its important to remember that all damage numbers given in the game are BEFORE shield mitigation/ armor reduction. One really effective thing you can do with snipe is use it as an opener and combine it with overcharge, before getting into close range. This gives you one free shot where there is far less shield mitigation, which allows you to inflict huge damage.
I thought about shield mitigation... but I don't think that was it... I tried an experiment to see.... I set up a game and invaded a pirate base with the Ragnarov and a support fleet of frigates. I don't think Pirates have shield mitigation, and there were no culture lines effecting it.
So I started taking pot shots at the orbital platforms, and sure enough, snipes were doing the exact same amount of damage whether they were over charged or not.... only 2600 points. If I remember right, the platform has about 3000 pts... maybe 3300??? Anyway, an overcharged snipe with my Ragnarov should have been 5200.... even with around 30% shield mitiagion it should have blown away the platform with one shot.... but it didn't... every overcharged shot I tried, only 2600....
Something is definitly broken with Overcharge