If a user account is disable or deleted in Azure Active Directory, you will still be able to filteron documents that were created or modified by the user or documents that were tagged with the user.
In a workspace where documents were tagged with the user account, before they were inactivated/deleted, you can continue to tag with the inactivated/deleted user, but you will not be able to tag documents with that user in workspaces where the value has not been used before. This is controlled per workspace/site in SharePoint.
This is unlike terms. If a term is deleted you can see it in the document list/view and you can click on it (filter), but you will not get any documents shown in the view.