They called him Ganondorf in Wind Waker, I believe. I'm not sure they ever called him Ganon, but I'm not positive. Anyway, the two are nearly the same now, so I think the names could be used interchangeably in this case.
About Majora's Mask, and TMW's suggestion as to who made it.
I think it's possible, but it was very thoroughly suggested in Majora's Mask that it was made by some ancient race, and more particularly by some shaman or witchdoctor. I don't think that necessarily discludes Midna from the get-go, but for now I'm going to doubt that she made the mask. It's reasonable to assume that she's somehow tied to the mask, but for now I don't think that's exactly it.
Also, they may have pre-planned the plots, but I wouldn't bet money on it. They're more focused on game elements, and as a writer sometimes I'll start writing a short story without knowing how it'll end. That sort of thing varies. At most, I'm betting they may have had an idea. I'm not really sure how much they'd plan ahead.