Hello,
I have just experienced the same problem today, and spent some time looking into it. The fact that it worked for @dgc when using the tagged release 3.9.0 was a hint that something changed in the meantime, and I think I have figured it out. Here’s the culprit: https://github.com/mattermost/mattermost-docker/commit/6512a09608c5a3566aa973c9359451d37023ea61#diff-7bfa124914e2e8affd23055295839cb8R14
This line adds an environment variable for the Email Notification option, set to false by default. I assume what happens is that this env variable always applies, whatever the actual value is in config.json.
Solution: add - MM_EMAILSETTINGS_SENDEMAILNOTIFICATIONS=true to the environment namespace of the app service in your docker-compose.yml file, and re-run the service.
I have filed an issue on github: https://github.com/mattermost/mattermost-docker/issues/140