This is an expected behavior, Smart IT install the notification and update some of the existing ITSM notifications during install. So if there are customization on the notifications messages it will be updated as well. (and therefore re-enable them if they were disabled) In future version of smart IT we are going to seperate the Smart IT and ITSM configurations and have a way to configure between them, that is in a backlog and not yet in any release target so it is coming after 1.3 release.