I noticed this too. Of course, it's fantastic that all these footprints are now there, let's make it clear we are not complaining about too many footprints! It's just a question of how to manage them.
For components, they have a description and keywords field. That works really with the Component Chooser (and I think dev builds have a filter box in cvpcb). I think a similar filter box would work well for footprints, even without extra fields, because there are keywords in the file name. So typing "MST ang" would cut to the list to a manageable number.
I'm not in favor of creating sub-folders, it's a very poor way of creating an indexed database. It would be really nice if footprints had description and keywords, even nicer if it was possible to add any meta data in a forward/backward compatible way (it's possible, but requires more effort than simply rejecting unknown data).
Adding fields is not an option until probably v6 now - many years hence. (If I was in charge, I would make the data file format forward compatible, but I'm not and it is not KiCad policy.)
But I think the situation can be improved by simple text search on filenames, which doesn't require significant changes to code, file format or repo layout.