Ok, I'm going to use venusaur with weather ball against golduck. This will be in the Sun. Let's see the damage changes.
252+ SpA Life Orb Venusaur Weather Ball (100 BP Fire) vs. 252 HP / 252+ SpD Golduck in Sun: 81-96 (22.2 - 26.3%) -- 13.9% chance to 4HKO
This is without cloud nine.
252+ SpA Life Orb Venusaur Weather Ball (50 BP Normal) vs. 252 HP / 252+ SpD Golduck: 55-65 (15.1 - 17.8%) -- possible 6HKO
This is with cloud nine. You can see that there is a large difference. Therefore, I believe that it does affect it.
Hope I helped :)