You assume 'old' strictly implies outdated, or bad, which isn't true. E.g. good passwords are still undefeated. And security protocol redundancies surely can make intrusion impractical, even if individual components fail.
I assume, military hard- and software to be made meticulously, double checking everything, on literally battle tested chips and gear. I mean, I really had no contact with anything military ever, so that's a guess based on aircraft and space development, pictures of überfunctional UIs and the ridiculous finances of the US military.
I don't mean to diss W2k in general, Its an OS that is well understood by now - weaknesses, mitigations, etc. Slowmoving entities like the government accrue so much cruft that it makes it exceedingly difficult to move to newer (and possibly better) platforms to take advantage of newer security tech.
And for W2k, I wasn't merely suggesting it's well-tested, but also a different, better thing than say WindowsXP. At least, I got the impression operating systems folks reference it for a "many good ideas" kinda thing.
Sorry, I don't have any expertise in any of this and talk mostly out of my ass.