Sometimes, cleanup operations adjust the tags (or category) of a large number of topics. In this case, the notifications sent out can be quite useless and overbearing. SImilarly, for topics watched by a lot of users.
I propose to allow suppressing notifications for batch operations, e.g. by adding a checkbox for that purpose to the respective form.
There is a disable_tags_edit_notifications (and a disable_category_edit_notifications) site setting which you can enable when changing a lot of tags/categories. Have you tried those?
I think the new bulk tagging modal also has a checkbox whether users should be notified. Did you use this and users were still notified?
