In the ArcObjects world, we can write a Workspace extension for a specific geodatabase. By using that extension, we can create hidden tables in that geodatabase to store some data about our internal business logic, so that the users cannot see and modify those datasets. You can take a look at the documentation on get_PrivateDatasetNames() by using the link below.
Is there a similar mechanism for ArcGIS Pro? How can I create hidden tables in ArcGIS Pro SDK .NET?