Minor necromancy because googling for a similar intent (see all books at once in KOReader ) lead me here, and there is an official answer now starting with KOReader 2025.04 "Full Moon" using KOReader Collections:
KOReader Collections can be populated MANUALLY from inside the collection's list from the 'hamburger' menu, choosing "Add all books from a folder and its subfolders"
Collections: add books from a folder koreader/koreader#12892
KOReader Collections can be populated AUTOMATICALLY from the list of collections, by long pressing the collection name and choosing "Connect Folders" then "Include subfolders"
Collections: connect folders koreader/koreader#13336
Note that in my experience with a large number of books in the directories (6700), ordering the collection by title or author took super long. 20-30 minutes long.
So I'm not sure how usable a solution this is.