The only "folder" you can mount for access by your PC is /sdcard. This is available even before you rooted.
All the other parts of the filesystem can only be accessed from the phone or with a phone app.
Not sure what you're referring to as a "hidden directory." In linux, a hidden directory is simply a directory with a period at the front of the name. When you list the contents of a directory, any subdirectory that has this naming convention will not be listed (unless you specify to show hidden files and folders in your list command).
An app like Root Explorer will show you these hidden files (aka dotfiles). Or if you want to get fancy, you can use Terminal Emulator, which will give you a linux shell. Or install QuickSSHd, which will allow you to SSH or SCP into your phone from your PC.