I have same issue. I would like to explaint my testing. I have 2 iphones:
1/ old iphone 6 (only for testing) - ios10.2 - clear new install - only my exchange account configured
2/ my actual iphone 7 - ios10.2.1 - this is my real iphone - this iphone has my every data from the past. I restored backup from older iphon - here i have same exchange account configured.
1/ new clear iphone 6 - doesnt have problem with email notifications (after unclocking, email notifications are still here)
2/ old backup on iphone 7 - have problem with email notifications (after unlocking new email notifications disappear)
I think this is problem with mess in old backups or something like that. But i dont want to start on new iphone 7 with clear ios. It is a lot of work to manually move datas to the new iphone. I want to migrade old datas to the new iphone with standard way as always from old backups (for example from icloud backup).
It means clear install doesnt have problem with mail notifications.
Old backups have problem with email notifications.
Please apple help us!
Miro