And it does imply a full directory lookup of the documents folder, and, as we all know, disk I/O is expensive, even on a flash drive

.
If you happen to have an empty kindle next to a Kindle with ~1K items, the slight difference in reactivity on wakeup is noticeable, especially in certain parts of the UI (collections, notes).
And if you check the CPU usage with top/htop, you'll notice that it'll churn @ 100% CPU for quite a while, compared to the 'empty' kindle.