apples to apples, yes. The same type of weapon, one size bigger packs a bigger punch.
I may be wrong, but I also believe the ammo is more expensive and the rate of fire may differ slightly.
the quickest way to check the differences is to go to your hardpoint on the loadout where you have the smaller one, go to buy a bigger one and use the compare button instead of the buy button, you should see every difference highlighted in either blue or red and the stuff that are the same in standard text.
