Please follow these steps to enable this feature:
1. Click on "Setup & Embed"
2. Click on "Preferences" at the toolbar
3. Under "Advanced Settings" tab enable the "Hide Empty Fields on Emails"
FYI: This feature will work only on default email template. If you edit/modify the notification email template, this feature will not work.
Let us know if you need further assistance.
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You are welcome, do let us know wherever you need our assistance.