Apps can be broken down into two types, those in:
- My Work
- All others places
(1) are unpublished apps owned by a particular user. There's no way to removing the app from the Hub without deleting the file on disk.
(2) for these, you would need to unpublish an app which would turn a (2) into a (1). There is no supported way of doing this, but you would need to go into the Repository Database and edit the Published value in the Apps table. I'd certainly backup the database before playing around with it.