I can’t imagine that’s the main reason. You can buy a 3.5" floppy reader with a usb connection for like 20 bucks on amazon and anyone who wanted to get their hands on government secrets would not be deterred by that.
I think the simplest and most likely reason is that updating things and making changes in bureaucracies is hard on its own, and any time you start dealing with tech it’s all a house of cards where one system depends on another and so changing any one thing will either make it all fall down or bring along with it massive sweeping changes.