I've been trying to figure out the notifications system, specifically where user notification preferences are stored. For example, UCP > Board preferences > Edit notification options, the check boxes for notifications and email for various notification types.
I thought it was maybe in the user_options column but I changed some notifications and the value of the number in the column did not change, so some bit flags apparently did not change there. Then I thought maybe it was in the user_permissions column but that did not change either.
I looked in the phpbb_notifications and phpbb_notifications_types tables but there is nothing obvious there.
Perhaps there is an article about how the notification system works.