"Born secret" and "Born classified" are both terms to classify the information of anything regardless of when and where it was created.
Real Life Example: Anything about the Manhattan Project relating to the Atomic Energy Act of 1946 was to be considered Restricted Data until appropriately declared declassified.
Equestrian Example: One of Equestria's interesting secrets is the Black Project called the Elements of Harmony. It is unclassified if it was created by the Royal Sisters themselves or if they simply discovered them, it is most likely these so-called Weapons of Peace where Born Classified.