From what I understand, which squares with the times I've been to the Pentagon:
* People working late at the Pentagon don't order pizza to the building
* The Pentagon has pizza options, including late-night ones
* The Pentagon is in fact chock-full of restaurants
* There is in reality no such thing as real telemetry about pizza orders near the Pentagon.
I have the opinion that this pizza thing is mostly just a story people tell because it makes them feel clever. Not high-horsing it; I have those too.
Not to mention, there's something like 25,000 people working at the Pentagon.
There are so many potential late-night work things happening that would need food, the idea that pizza orders can be used to identify high-profile military missions specifically doesn't make a lot of sense...