Japan's government has finally eliminated the use of floppy disks in all its systems, two decades since their heyday, reaching a long-awaited milestone in a campaign to modernize the bureaucracy. By the middle of last month, the Digital Agency had scrapped all 1,034 regulations governing their use, ...
If it works well for the job that it's tasked to perform, why change it? It's got the added benefit of being an unintentional security feature now too, as very few others will even have a drive for reading them. Sort of like how manual transmissions are much less likely to be stolen now.
On the other hand, if you use an old technology that isn't being mass produced anymore, it can reach a point where it will become a big liability for a mission-critical piece of equipment.
Yah this is bad I run a cnc plasma table, big table 10 feet x 20 feet. It uses floppy disks. Pain in the ass to find a new drive and pain in the ass to find new disks because constant write re write emf and metal dust kills them. But despite that it's still cheaper and easier than a $15k retro fit to a more modern controler.
Your example is one where it clearly isn't a great fit for the job. If you wanted to transfer sensitive data discretely, a floppy could be significantly better than a wired network where you've got to worry about America/Russia/China/Israel/Iran and who knows who else peeping on the transfer, or a USB drive which is already known to be compromised by stuxnet derivatives.