Only most of the amounts were tiny, so all the effort for the re-calculation was still needed for everyone (basically either building a payroll engine from scratch, or paying someone else to use theirs). You're right, that for most current employees, for the small amounts it actually is much simpler. You can just email and slip it into the regular payroll.
It is the former employees for up to 15 years that make the contacting step difficult. They all need to provide bank/tax details.
There are also some current employees who still have to provide details before they can be paid. The company I work for has a lot of people moving countries, and therefore tax jurisdictions. In addition, some employers decided it was worth asking if employees were prepared to voluntarily allow offsetting between the overpayments and the underpayments, as in some cases those were quite large.
I can understand not wanting to give large amounts of money where it effectively would just balance out, especially after spending staggering amounts on the recalculation itself. There are government departments that have been working on it for years (or perhaps worse, and paying consulting companies to work on it).
Edit: I should have said, I did see companies rounding all amounts up to some small amount, like $1, so your suggestion is good. It just doesn't save effort on recalculation, or much effort in getting people to dig the email out of their trash folder and provide their information to receive their $1.