Our company policy doesn't allow to delete any issues so I modified Service Desk permission scheme - I removed almost all Delete Issues permission entries.
Now I got warning that This service desk project may not work as expected. (screens attached)
This dialog is visible all the time for both Project Administrators and Agents.
Additionally Project Administrators can revert JIRA Administrator's changes. According to me they shouldn't have such possibility but it is another issue.

I think that such changes should be possible and notification should be displayed only once just after change and disappear after confirmation and shouldn't bothering other people especially agents who doesn't have to know technical aspects.