I was mostly thinking of the physical design of the ships (and their operation) as brought up by OP and GP. But even when it comes to IT, I can understand having a hard time fully validating a new OS on those ships. And still they take much better measures for securing those carriers overall than your average supermarket with XP cash registers.

The point, as I said below, is that the framework under which the military operate does a far better job at forcing the people to more consistently adhere to stricter rules. Which means under similar circumstances there's a good chance the military can keep a system safer than most companies.