Any apps not saved to the cloud are lost unless the files were stored on a network share, or other internal share. (It may be a good idea to establish a shared file location for app files which are not shared to the cloud.)
Apps that have never been shared with other users will remain inaccessible by the org.
Apps that have been shared with contributors, can continue to be edited and reshared by contributors, even after the original owner leaves the organization
The App will remain orphaned (as to an Owner) if the Owner drops out of the directory. However, this does not prevent contributors from editing and resharing the app.
We are definitely planning to enhance the methodologies around app ownership so that apps are not orphaned when the owner drops out of the directory. In the meantime, it may be advisable to establish internal policies to ensure there exists more than 1 contributor for the apps that are designated to be used broadly within your organization (perhaps this can be facilitated by using security groups for contributor members).
Thank you for your continued feedback and support as we enhance the admin experience,