When I connect my fairphone to my laptop, I can’t find NoteBook or Messaging files to copy them to the laptop?
Does this help you: SMS Backup+?
I’m afraid notes can’t be backed up because the notebook app is modified by Mediatek. Maybe someone els knows a solution though! 
Have a look at this topic which should help with the notes: Does "Backup&Restore" backup my notes in the NoteBook stock app?
When you refer to the messaging files, are you talking SMS/MMS? If so you can use the default “backup & restore” app that is on your phone to save these. This is under the personal data section of the app
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