Hmm...not sure why there'd be a need to "close" a folder; they don't really get in the way at all, and I've never done it in the year I've used it.
For me it is a case of visual distraction. If there are tabs at the top of something, and I'm only going to be using half of the tabs, I prefer to only have those tabs I'll be using visible.
Useage-wise, it was totally counter-intuitive to how other Microsoft tools work that include a project space. They made it feel like closing a file from the view, yet really deleted it from the project. Microsoft usually does a really good job of providing coherent interfaces across different software packages, so I blame it on the fact that One Note hasn't had that many releases of polish yet.