The iOS limits the number of apps in the "Open in..." list to 10. If you have more than 10 apps that can handle a document, the iOS will simply skip some of them. There is nothing we can do about that, unfortunately, and the only solution is to delete a few other apps and thus make Notebooks appear in the list.
The iOS then obviously keeps track of how often an app is used in "Open in..." and shows the favorite apps at the top of the list.
By the way, this issue is not specific to Notebooks, it affects all apps. Apple's discussion forum has several threads covering this:
https://discussions.apple.com/thread/3073437?start=0&tstart=0
https://discussions.apple.com/thread/2679947?start=0&tstart=0