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?
Unfortunately, this functionality is not included in the Pro SDK, and we don't have any near-term plans to add it.
I cannot think of any sure-fire workarounds, but you might be able to get by with some of these ideas:
None of these give you what you had with workspace extensions, but I hope they are useful ideas at least.