Personally I thought this filler was the most interesting out of the fillers. Sure the fart was dumb but we all knew that the Bikochu mission had to fail some how. Adding in the humour was much much better than the lame baka brothers' jokes.

As for why Hinata was using the water for her training: same reason why Domon Kasshu needed a drop of water to get his concentration and why Ninjas like to train underneath waterfalls. And she was naked because she didn't want her clothes to get wet. (other than satisfying fans who wanted to see her naked......Hmmm)

And Kishimoto does not have any says on the anime at all. The rights have been sold to the animation company, and the only credit he gets is that at the beginning of the show it states : "Original creator: Kishimoto Masashi". He might get money based on the viewership and so on, and maybe an advisor to reduce confliting plot advancements in the manga, but that's about it.