Processing 500 books on my Kobo Mini seems pretty fast. Maybe a minute or two.
But they are not on an SD card.
On my Sony T1 processing 1000 books in main memory is pretty fast, again a minute or so I think, but 4000 seems to take forever.
Processing 10,000 on an SD card would probably take a very long time. Pretty sure it would be the same on a Kobo Glo. Plus if it crashes, which does happen, it would probably have to do it all over again
Like yourself, I think the indexing may be unnecessary as there are 'fixes' to prevent it on the Sony readers, but I do not know this for a fact.