Actual national security concerns. A WW2 example, if you knew where the enemies communications station was on their ship it made for a good target. If FOI in peacetime releases this information for some article, thats the enemies job half done.

Also, Commercial in confidence is a real thing, its called Privity of Contract. It means parties to a contract have a right to privacy in their dealings. Whether this is right or wrong, it has a long and strong legal standing.