REST api is supposed to replace XML/RPC and SOAP APIs which are already deprecated (and contains blocker bugs).
I am filing this as a bug because it is clearly a regression from using SOAP where you can skip sending notifications.
This bug makes maintenance via REST almost impossible due to the amount of emails it will send to the users.
Support suggested disabling email notifications while the scripts are running but that's not possible for two reasons: these are live systems used 24x7 and 2nd, these could be triggered at different times or scheduled to run periodially, it's not possible to disable email notifications for the entire instance just to prevent these from happening.
One possible solution to this problem is to have a special group, like jira-bots (or jira-automation, jira-silent) for which jira will skip sending email notifications if the changes were made by a user part of this group.