Firstly, Cloud Nine does not cancel out weather, it cancels out its effects. So weather can always be set up if there is Cloud Nine active it just wouldn't do anything.
Naturally, the next question which comes to mind is whether the weather set by a Pokemon with Mold Breaker be active. The answer is NO, because Mold Breaker doesn't disable the opponent's ability, it skips the ability check while using a move on a Pokemon. Since weather moves and Cloud Nine both apply on the field not a Pokemon, Mold Breaker has no effect on them. However an ability that disables the opponent's ability (Neutralizing Gas) does stop Cloud Nine from removing the effect of weather.
