One could argue that the Yamato's would fall under this category.

The ships were constructed so secretly that military police would patrol and enforce the boarding up of windows that faced the shipyard. While she then spent much of her career at anchor at Truk, far away from curious eyes and recon assets while the war went in Japan's favor.

In fact it was not until February of 1944 that the Allies were able to take their first photo of any kind of one of the ships. While through intentional mislabeling the size of her guns was a major question mark. Though her size indicated 460mm or 18.1in guns, the IJN referred to them as "Special Type 40cm" or 16in guns. Meaning that many officers in the IJN itself had no idea how larger her guns actually were. It was actually the interrogation of Admiral Yamamoto's former Yeoman, captured on Saipan, by Ed Layton(famous for serving as Nimitz's S-2 or Intel officer) that revealed the deception.

Navweps gives a solid chronology of the discovery of the facts of the class here: http://www.navweaps.com/index_tech/tech-084.htm