The article is a little ambiguous about the nature of the information that was stolen. However, I used to work on the Space Shuttle program at Rockwell in the early 90's, so I think I can read between the lines a little here. When I worked on the Shuttle, it was, and probably still is, and entirely declassified program. I was not aware of any part of the Shuttle that would be considered even secret, let alone top secret or higher. I'll reiterate, that I was not "aware". However, I worked in a central data management department. I had access to almost the entire design documentation of the shuttle. I had a secret clearance so I could work on other space programs. Therefore I think that if there were any secret documentation related the Shuttle I would have at least known about its existence. Back to the ambiguity of the article... I can easily see how Boeing could be the one harmed here, not the Federal Govt., as there was a lot of proprietary design in the Shuttle. If that was the sort of information that was being stolen then this is not a matter of national security, its a matter of stealing competitive business methods and information. That is an entirely different issue. Anything that was designed and built by a company without the use of tax dollars, including the design of a light bulb, could have been considered proprietary in the context of the Space Shuttle program.
If this is in fact a matter of national security, then I think it is far more likely the secrets stolen, if any, had to do with the payloads the Shuttle has carried. Prior to the Challenger accident, the Air Force used to use the Space Shuttle to boost classified payloads into orbit. Most of those payloads and the associated missions were classified.