Where I work, there is some lab equipment run by Windows 95 computers, because the software that runs the machines just won’t run on anything newer. It’s entirely possible that something similar is the case with Black Mesa, Breen doesn’t want to spend thousands of dollars to replace perfectly good, if a bit old, machinery, when the money could be better spent on some more important improvements to the facility.
Like a Scrooge McDuck vault right next to his office.