I'm not sure anyone can explain it. Author Aimee Bender:

"What a surprise, then, to find that there is a blank page with 'Goodnight nobody' out of nowhere, sharing a spread with 'Goodnight mush.' [...] 'Goodnight nobody' is an author's inspired moment that is inexplicable and moving and creates an unknown that lingers. [...] I feel sure I will never crack open the meaning of 'Goodnight nobody,' and moments like that make rereading a genuine joy."

https://opinionator.blogs.nytimes.com/2014/07/19/what-writer...

But for what it's worth, I think it's there for a simple reason: to reassure children that there is nobody else in the room, nobody else to fear.