We have a "Restricted" folder functionally that we created which
- Allows a folder, or folders, to be specified as restricted in the Files section.
- Once set as Restricted, only Administrators can view that folder and its children.
- The restricted flag is set recursively on all children.
- An extended or replacement (can't remember which) version SiteTreeDropdown enforces this view in TinyMCE and other interfaces that use the TreeDropdown to view files.
We've always thought that the hardcoded /assets folder is annoying, so this feature allows us to put files into the /assets folder whcih are managed by ModelAdmins or other interfaces without "cluttering up" the files DO need to be managed in the Files section such as files uploaded for use in Content.
This is definitely not a module quality implementation, but if you are interested I could pass along the code so you could use it as a potential starting point. Since I don't understand the full context of your need here, it may or may not turn out to be useful.
On a separate note:
We also have a method for creation of files in a folder outside assets and delivery of those files via php action rather than direct download in order to obfuscate the actual location, but that stuff is more trivial than the restricted folder stuff inside assets. In our case we generate the file in /temp folder, deliver it via an action (direct download not allowed via htaccess) and then delete it after 30 minutes via a cron.
However, this is not a paid content delivery system and we have other requirements which is why it works the way it does, but it seems similar to what Josue described as being the current state of things.