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Bulbapedia states nothing on the matter, while Cloud Nine is stated to remove all weather effects.

Please don't question my curiosity.

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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 :)

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You said it will be in sandstorm but the damage calculations say fire
crap yeah I mistyped. Thanks :)