There is an exception to the FOIA for classified documents. But that does not permit the Government to ignore the request-- they have to respond, on an item-by-item basis, and either release the document or assert whichever exceptions they think are applicable.
This judge did not order the Government to turn over any documents-- he ordered them to respond to the request. This is a valid order and will probably be upheld if it is appealed. I assume the Government will respond by asserting the national security exception.
Interesting ... thank you.