Can messages be created/updated via API without triggering update notification emails?

Hi cgrinton , in this scenario you could temporarily stop email notifications in community by using a setting in the Admin settings under the Maintenance tab. Refer to this for more details.
Once you are done updating the messages, you can enable email notifications again by turning off the setting. 
Please note that using the setting will turn off all email notifications, except account related emails like those for user registration, password reset, and email update notifications. Hence, make sure that you disable the setting once your work is done.