Did a side by side comparison of the big shot (as nobody honestly cares about the little shot). Findings were what I personally was expecting. Both guns are level 10, no UVs, no damage boost from armor.
Test subject was a Depth 27 Slag Walker.
Polaris did 110 damage from the big shot (still bugged to be normal damage, once fixed it will do quite a bit more obviously against Undead).
Supernova did 129 damage from the big shot.
As expected theh Supernova has a higher base damage even though the 2 bars are identical. You pay for the shock possibility with a lower base damage. Seems to be the standard rule on weapons... if it has a benefit against a certain monster type (CIV vs Levi Blade) or can inflict a status (any elemental alchemer vs prismatech) it will do less damage even if the bars are identical.
~Gwen
This is useful information, thank you. Still, even though there is a damage loss, it doesn't seem to be enough to make a significant difference on average.