Why do people think this? They directly stated that Bayonetta was the overall winner. What would Sakurai and Nintendo have to gain from lying about this? Do people actually think that Sakurai has some secret vendetta against K. Rool or wherever else you think "really won," to the point where he would make this big cover-up? They had the ballot to determine who is the most wanted character, and by extension, who would bring in the most money. By staging Bayonetta as the winner they have nothing to gain, and money to lose.
There's two options to explain why Bayonetta shockingly won:
1. The people who spend everyday, for multiple years, making sure this game is as good as it can be, lied to all the fans, just because they don't like a video game character, even though they would theoretically lose money by making a character who scored lower in the ballot the one you can buy.
2. The couple of dozen or hundred people that post on this forum are actually a really small sample size compared to millions of people that probably voted in the ballot.
Anyway, I still think the ballot was partially made for future Smash games, including the one we're getting this year. I am still fairly certain that K. Rool was up there (along with other characters they made into DLC costumes like Chrom and Lloyd Irving) and think he has a decent chance for this game.
But yeah, the ballot wasn't rigged. This isn't like a political election where someone has something to gain by rigging it. The only reason they would lie is because Sakurai hates a specific character that much. Even then, they could've just not named Bayonetta as the #1 winner if she wasn't and they wanted to hide it.