I started out in a very small but rapidly expanding software company, where the founders encouraged everyone (including themselves) to be very open about salaries. This didn't work too badly because most employees were recent graduates and no-one was earning much money. However it did generate some dischord when it became apparent that those from less prestigious universities were getting paid slightly less.
A few years later I was working in a very large corporation, where (like you), HR hadn't secured their data very well, and I got to see details of many thousands of salaries and bonuses, including those of some of the highest paid people in the UK at the time. Without going into too much detail, the remuneration disparities were staggering. I think it is fair to say that it was the sort of company that was prepared to pay as much as necessary and as little as possible. If the scale of inconsistencies were widely known, I would imagine it would have created a fairly toxic working environment.
So in the end it might come down to company size and culture. I can't imagine why a small coffee shop, like in the original article, would want to keep it so secret though.