Open Government Advocate Steve Aftergood has provides some numbers on USPTO Secrecy Orders. [FAS BLOG][New Data]. According to the USPTO FOIA response, over 5,500 pending applications are currently held in limbo under a secrecy order. Because the inventions are being kept secret, we cannot know whether the secrecy order is a valid exercise of government power. Aftergood writes:
There is nothing in the raw numbers that would provide an indication of the validity of the decision to block disclosure of a patent application, whether a secrecy order was appealed or challenged, and what adverse impacts, if any, such an order might have had.
Some recently declassified inventions include a really interesting RADAR cloaking device that is now protected by US Patent No. 8,836,569. See also MPEP 120.