Actually, I found two ways of fixing this problem.
First one: you can merge all the index_splits into one, rename the merged index to remove the nested directories from it (the /1/1/ stuff), and split the indexes again with "split at multiple locations" (RMB in the editor). In my case, I split books with h1 headers.
After that you rename everything with bulk rename if you want to and the nested directories will be gone.
However, the shortcoming of this option would be that you can't do anything to the nested directories of the images. While renaming two CSS styles is easy and not time-consuming, there can be a lot of images in the book(again, in my case, there are a lot of them) so the /1/1/ thingies remain there.
The second way: this way means not to create nested directories at all, meaning, to not use the plugin for merging books(I'm sorry plugin creator
...) But how do I merge the book? You ask. Well, I've found an easier way to "merge" the books. You simply copy everything from one book and paste it into another. (I know, I know, why the hell did I not think of it before...) So basically, in the editor, you select your indexes, styles, images, or whatever else you need, then right-click and select copy, go to your other, let's say "main" book, and right-click where indexes are shown, and select paste. (do not close any of the editors while you are copy-pasting, because otherwise it will not work and you'll encounter an error) Voilą, you just "merged" the books! now you can reposition index_splits as you wish and fit to the book's needs.
However, you should know that new index splits won't generate ToC this way, so you should go to the "Edit ToC" and use the tools provided to get the full ToC again. I use headers for chapters all the time, so it's pretty easy for me. If your book has a good or "correct" structure, you shouldn't have a problem here. If you fine-tuned ToC in some way before and don't want to lose it, you should just generate a new ToC in the manager and delete duplicates, only leaving the new index splits(the chapters you just merged)