As per the explanation on
JSD-1961, it would appear that if the "email request" functionality is disabled for a service desk, that comments emailed in by participants in response to system-generated emails are automatically marked as internal and thus hidden from the participant when they go to view the ticket activity within the "Request" area of the service desk.
I would request that this functionality be changed to provide administrators with the option to allow these comments to be displayed publicly.
We use (and love) service desk because it gives our non-technical users an easy way to enter tickets but still allows us to ensure we get all of the data we need to fulfill a request. Turning on email submissions allows our users to side-step those required fields, and so we absolutely do not want to turn this on. However, users are replying to system-generated notifications with comments and then get confused when the comments they send in are not displayed when they pull up the activity in the lite "Requests" section of the service desk.