There are hidden files and hidden folders scattered throughout the file system, and in user-level directories too, not just system-level, restricted ones. A typical example is a .nomedia file that any user at any level of permissions can add to a folder if they need to. Whether a file or folder has system-level or user-level restrictions on it is determined by its permissions settings, not if it is or isn't hidden.
Most third-party file manager apps will have the capability to show hidden files/folders. The default setting might be to not show them but can be enabled/disabled in the app's settings menu. But hidden files/folders are almost always meant to be hidden, the intentional purpose being so most people won't mess with them. So be very judicious about what you do with hidden files/folders. If you're not sure about a particular hidden file/folder be sure to look into why it's there before deleting or modifying it.