Floppy-disk based systems are not the only way to ensure security/reliability, but it's far better than a half-baked system that isn't properly audited. Systems we rely on must be dead simple and reliable.
There was no alternative to floppy disks when they were built though. Was there a deliberate choice to use an older technology?
I'd assume that's more about not fixing something that isn't broken. (Because if you break it, you might accidentally annihilate humanity!)