OneNote Class Notebooks created with SharePoint app v created with App Launcher in OneDrive

Hi there. I cannot comment on which will be supported, but if I were a betting man I would say that (A) will be phased out. One of the challenges of (A) was that it required ICT in many schools/organisations to create the Sharepoint sites that had the app installed. In most cases, this wasn't how teachers and ICT interacted and bypassing ICT actually dramatically increased the use of the tool (at least here in Australia!). 

Given the direction with Microsoft Classroom, I would imagine that (A) will most likely turn into MS Classrooms (based on Office Groups). Office Groups/Classrooms come with their own set of challenges, which then leads us to School Data Sync. If you are a school with a fully functioning SIS/SAS feeding into School Data Sync those 'hit by the bus' scenarios (teacher sick, teacher leaves, teacher quits, etc) become less of an issue.

To answer your final query the easiest way to move notebook from (A) to (B) is actually to simply copy and paste sections etc. You can do some other workarounds, but I generally teach my teachers that method because its easy and because it is applicable to other activities. Generally most of our notebooks have less than 20 or so sections in them, so the process just involes a little moving.