San Francisco resident here. As far as I can tell from all the various things I've read, the news surrounding this issue is badly reported based on interviews with uninformed and technically un-savvy public spokespeople.
I mean, some of the stories talk about needing to find programmers proficient in "90s-era programming languages." Which ones might those be? I'm unaware of languages that were widely used in 1998 and are completely obsolete today. I'm betting the real challenge is finding programmers proficient in C or even assembly language for embedded systems based on obsolete processors or microcontrollers. That makes sense, but the mainstream press doesn't report it that way because they can't understand it,
So I really doubt the floppy disk issue is a significant problem (and I'm even dubious of the claim that they have to boot the system from floppy disks every night). It's just a savvy PR hook to gain public support for the funding they need to upgrade the entire train control system.
Read here for an official press release from the transit agency that explains the main issue is replacing the extremely antiquated wireless communication system that the trains use now. It's a hardware and networking issue, which naturally needs entirely new control software as well, but not really anything to do with storage media.