Unlike Pinkie, Twilight actually read Cupcakes all the way through, because, well... She's Twilight. She's never met a piece of literature that she didn't finish, no matter how horrifying Cupcakes was proving to be.
Directly after reading it, (and possibly after vomiting a few times,) Twilight had to go check on Rainbow and Pinkie, waking them up to make sure everything was alright. Not wanting to upset her friends by telling them about the foul story, (and unaware that Pinkie had already read it,) she made her way back to the library to try and figure out who had written the awful tale.
A few hours later, and coming up with nothing, Twilight realized that the sun would be up soon, and she should probably get some rest. But she was still plagued by the story in her mind, and the thought of laying in her bed by herself in the dark frightened her. So she slipped into Spike's basket, hoping that being next to her little dragon would help her sleep.
*I read a comic version of Cupcakes While in equestria* (Fan based version of me) And what was my reaction? Rushing up to cloudsdale to see if Rainbowdash was ok
i also slept in the doghouse with my dog after reading the fic. he's the only being i really feel safe with.