Many people wonder why there is no Phantom Bonnie in FNAF 3, and then proceed to make complicated theories with paranormal stuff, using little to no real evidence from the game. I have decided to offer a simpler and more realistic theory.
There is no phantom Bonnie because that would be too many Bonnies. Lets count the Bonnies: There is Bonnie from FNAF 1, Toy Bonnie from FNAF 2, Faceless Bonnie from FNAF 2, Shadow Bonnie from FNAF 2, And Springtrap from FNAF 3. (Yes, I know Springtrap is not actully Bonnie but it is an earlier model of Bonnie so I'm counting it.) Altogether, that is 5 Bonnies. Compare that to the 5 Freddys. (Freddy, Golden Freddy, Old Freddy, Toy Freddy, and Phantom Freddy. If there was a Phantom Bonnie, the Bonnies would outnumber the Freddys, and that would be a little too much Bonnie for a game called Five Nights at Freddy's.
Also, Scott has said that Bonnie is the only animatronic that really scares him, and that Bonnie has given him nightmares. Perhaps Scott thinks making a Phantom Bonnie would make Bonnie too scary.
So, thats my theory. If you disagree, please comment. (If you can comment on blog posts. I don't really know how this whole thing works.)