Hi USA80,
In the Sitemap Designer under Advance Tab of subarea Properties, the Privileges feature can help you.

https://learn.microsoft.com/en-us/dynamics365/customerengagement/on-premises/customize/create-site-map-app?view=op-9-1#add-a-subarea-to-a-group-in-the-site-map
You want to hide one entity from the navigation only, but can use it on other place, so you can use other entities' privilege to control it.
Steps:
1.Create one custom entity.
2.Go “Site Map Designer” page, select one entity(subarea) you need.
- On the right side, under the properties window, click on Advance, then on Privileges. Select the entity we created earlier, and then click on the “+” button.
- Expand the command and check only the Read command.

3.Set security roles:
(1)If the user needs to see this entity(subarea) in the navigation, you need assign 'Read' privilege to them.

(2)Conversely, it is not used.
For users who do not have read access to the custom entity, the entity will not be visible in the navigation, but will still be available elsewhere.