They should have stayed rare, but they’re a way for universities to get free money from the government as well as a temporary (but sadly permanent) fix for academia’s deep structural problems.
So Yale's PhD count grew a bit, but nowhere near as much as the rest of the country's.
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But mostly, PhDs used to be way rarer in the back in the 50s (along with college degrees in general). If you look at Figure 1 in this NSF report (https://ncses.nsf.gov/pubs/nsf25300/figure/1#), it shows the number of PhDs tripling in just 15 years from 1958 to 1973. After 1973 it slows down to merely doubling over the next 50 years.
Admin growth might be a factor, although I'd want to look at national data first. Your own article says "... Yale had the highest manager-to-student ratio of any Ivy League university, and the fifth highest in the nation among four-year private colleges" so maybe it's an outlier.
63 years ago, they were rare, but my father was able have his professor and department secure funding within a few months. ( yes, Engineering has a lot of money available from the defense department ).
50 years later, the Molecular Biology postdocs were not so lucky. Not even an honorarium. "Maybe in a few years..."
For the most part, it’s just another artificial rung the system uses to justify exploiting people.