Unix(tm) and mainframes predate windows server by a far margin and was never seen as inferior to windows by the wider sysadmin community, there might have been a time when windows server had merit as the discount solutions for people who could not afford highly available Unix boxen, but it was never seen as superior or particularly well suited for critical infrastructure.
I think that's kind of whats in play here, few finance systems were designed as critical as well finance was that department that generated a few reports that nobody really read and rarely interacted with the core productive business to the point where flaws/bugs in finance systems could have an real impact until very recently so what you have is a bunch of aging discount/non-critical system that have been promoted to critical infrastructure nearly by accident.
The same goes for the desktop support infrastructure build around AD and SMB file shares, where systems that used to be auxiliary nice to have for clerical workers ended up as critical for the actual productive divisions without ever receiving any real hardening.
*nix OSes may have been as far superior to Windows as you can imagine, but the development ecosystem certainly wasn't. There were Delphi, VB and other RAD tools for Windows, with tons of GUI and general purpose libraries and toolkits. Bun on *nix you basically had just GCC and vim/emacs. There were no GitHub, no npm, no AWS, nothing. If you'd compare TCO of an enterprise app plus necessary infrastructure, the Windows-flavored one would come a clear winner. Even mixed environments were too much of a hassle, due to poor interoperability.
I am not sure what the registers ran, but they were IBM, all text-based.
Also, I remember my friend was a manager at AMC theatres at the time, and their system was entirely text-based. I remember watching him run end-of-day reports and you could see it zip up the files and hear the modem dial out and connect to corporate.
I dont think i can recall any commercial Unix even shipping gcc back in the day.
I have personally been involved in more java fat client then activeX based fake webapps, but im also not an wintel admin with an background in non-critical mid sized business applications.
Trumpet Winsock was a very important piece of software for a bit, from Windows 3 to 98.
Serial ports were much more popular back then.