git has hooks for access control (which is how e.g. gitolite manages permissions, albeit at the whole repo level - I'm not familiar with an open-source hook that does directory level).

With respect to hiding, git has sparse checkouts that can give you a limited view of a repository (for performance reasons - not for security reasons)

But that's just today's git. Other VCSs like perforce provide much finer grained access control and hiding.