Most likely - storm bolter is in essence an automatic pistol for a marine in terminator armor, while an assault cannon is a massive support weapon, equivalent more to the vanilla autocannon for an x-com soldier.
As for how 2-handed penalties work, there is a default reduction in accuracy for using a 2-handed weapon in the off hand, any exception to this is explicitly defined in order to display a weapon like a 2-handed item but have no penalty. It doesn't matter what the item in the off hand is, it just matters that it exists.