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I assume it was some combination of reading the metadata and the sorting. Connecting dir (plus subdirs) took reasonable time and reported the correct number of files.
At the time, I was using 9 (poorly balanced) subdirs and rather lengthy titles that I'd plugboard'ed into the kepubs to also have word count and all tags (to kludge metadata for Kindle/Nook).
I've since switched to a flat level dir with 6700 epubs and just title (+word count) in the epub title field. Files are named from Calibre {id}, so 100.epub, 13000.epub, etc.
A new collection linked to that dir sorts by name quite quickly; a second or two. Takes longer (5-10s) to open the collect, or the dir in file browser.
Sorting the collection by title just took 53 minutes.
At this point, I'm using KOReader; but I'm using the History and Search Calibre metadata features to avoid the file manager as much as possible.
I'll try to time the Extract and cache book information option tomorrow.
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