1. Illusion discs and their purpose

If it wasn't for the books we would've never known or understood what these discs were. (Twisted Ones -Fourth Closet)

2. Why Elizabeth liked Circus Baby so much

It wasn't because she was fascinated by Baby or liked ice cream. It was because William gave more love to the robot than her. To the point where Elizabeth wanted to be Circus Baby so she could be the center of her father's world.
(Fourth Closet)

3. Ages of 3?game characters so far

Charlie is 3 confirmed by Liz and her grave matching the fnaf6 one. Fourth Closet)
Elizabeth is a kindergartner (pg 304 Fourth Closet)
Susie is 8. (Coming Home)

4. Why William killed kids

It wasn't because he lost his family or was controlled. It was because he wanted to become immortal and used children's souls in hopes to become immortal.

5. Who Henry and Charlie are

We would've been really confused in fnaf6 since we wouldn't know who HRY is or anything about Charlie.

6. Heavily hinting at Mrs/Mr Afton being divorced

A perfect example to this is Step Closer, Hide and Seek Where the characters represent closely to the Aftons and the parents being divorced.  Another perfect example is Mrs Afton never appearing anywhere in games or books similar to Mrs Emily. Of course if she's divorced and avoiding the pizzerias she isn't important to the lore because she isn't impacting or causing anything to shift the story.

7. Soul splitting and body snatching

The souls are capable of moving into different bodies. Andrew  and Jake are perfect  examples. Andrew wasn't always in stitchwraith he was in other animontronics before he settled inside. While Jake was in a plush/doll whose face was used to be Stitchwraith's.

We saw in a bunch of stories like Lonely Freddy, To Be Beautiful, Fourth Closet CB the animatronics ability to body snatch/masquerade as someone else. Which  seems to be the somewhat case with Vanny right now.