Now that you mention that, I think that those that do not have changed the setting in their profile will have the default value (that should be simple notification).
There is actually a discrepancy between install and upgrade, because in the first case the defaults are inserted into the db, while in the upgrade the defaults are missing and only the existing notifications are converted.
So you can try with:
insert into {db_prefix}notifications_pref (id_member, notification_level, mention_type)
values (0, 1,'buddy'), (0, 1,'likemsg'), (0, 1, 'quotedmem'), (0, 1, 'rlikemsg'), ( 0, 1, 'mentionmem');