Hi Alan
I think the main point is that there were so many obsolete and logos there, and hardly any new ones. There were also wrong logos (after changes of operator without a registration change). I haven't got the time or inclination to monitor and update the world's general aviation fleet, and no-one ever posts or sends me updates for them, except occasional requests for new ones. As you say, no-one much cares about the disk space that these logos take up, but the wrong'uns are a problem that hardly anyone would notice - probably the worst kind of error. I don't think anyone has ever requested logos for new aircraft joining clubs, schools or companies for which we already have a logo, so there are hardly any new fleet aircract registrations represented since the original logos were done, often many years ago.
I'm happy to create and update the logos for operators, but keeping logos for individual registrations up to date is too large a job. Of course I too have copies of all the zips I've posted on my downloads page over the last few years, and users are welcome to contact me for old versions (the most recent pre-purge one was dated 22 February this year).
No-one has to implement these deletions, and installing new All Logos zips won't delete anything at all if users just use copy and paste, replacing existing files and adding the new ones to keep up to date. (Some of the oldest ones may still be in the software install package.)
As for military aircraft, we have very few individual registration logos (except for exceptionally interesting, usually historic, ones such as some BBMF aircraft), and mission codes (and ICAO codes) are safe!