For a project which is associated with ServiceDesk, if a user creates a Service Desk Request (through the Customer Portal), then notifications are sent correctly according to JSD-323.

However, if an issue is created normally by clicking on Create Issue button (same project) or via email through a mail handler (same project, no matter Default Reporter or recognized user), then the Reporter does not receive any notifications at all, including Issue Creation, Issue Updated, Issue Commented, and Issue Resolved.
This does not happen when ServiceDesk is disabled, hence ServiceDesk must have affected JIRA notifications in an unexpected manner.

Please take note that in all of the above situations, Notify me is On for the Reporter all the times. This raises a question with the way ServiceDesk handles notifications to Reporters: even though they purposely want to receive notifications for their own changes, they can't.