When using a neutral element cannonball, the element damage modifier for an elemental or endowed weapon will be applied for weapon/equip attack (as with normal attacks) and then the element damage modifier for a neutral attack will be applied to the whole damage - this means it will always miss ghost 3/4 monsters. This is the same as pre-patch behavior
When using an elemental cannonball, the element damage modifier for the element of the cannonball will be applied for weapon/equip attack, and then the modifier will again be applied to the entire damage.