I've JUST discovered what I think caused these deletes.
This site has multiple (more than 30) sites as sub-domains. I'm just in the processing of setting up a new additional site, and as part of that process discovered at Step 3 the "Scheduled tasks" item, with "Users delete non activated user" which is checked by default. Checked a few of the existing sites for that site-specific scheduled task, and YES, it is enabled for some of them!
These sites have been running for a number of years, and this has never happened before. As I said up above, the only other thing that has happened was that Hotfix 51 was applied approximately 1 month prior to my discovering the problem.