As for SD cards, ones that are more than just storage (e.g. with wireless technology embedded) already exist.
If its an embedded system and the cost and work of supporting it is less than the cost and deployment of a new system, whats the point in updating it?
The problem is support and maintenance. Things wear out eventually, and if you can't get the parts to fix them any more, then your whole system fails.
This really shouldn't be a problem with EEPROMs, however; I'm pretty sure you can still buy those, and the programmers for them too. But 8" floppy disks, and the drives to read them, are another matter.
Nah, this is a scary example of critical capabilities depending on legacy hardware people might not dven make that they're afraid to replace. Sandia at least modernized some of our nuclear system. They need to deal with this, too.