And here I was prepared to wait it out for months to years, thanks for reconsidering. I made experiments with the above mentioned Advanced renamer program. It is great, because it shows all files in the folders you drag and drop in in the order the folders are sorted. so folders 1, 2, 3 with the same filenames within each folder show up after one another.
Here is how it looks like:
http://imgur.com/a/m97d9
That allows for very easy way to run a rename batch, which goes through the files and sets a number.
If something like that could be implemented using kcc, it would be truely a blessing for kobo users. Further I don't know if it could cause errors, but a kobo mode should have all images in one directory, without subfolders. The kobo aura hd reader can read numbered files properly, even when they are spread accross many folders (e.g you batch renamed all files so they have a unique number, but they are still in their chapterfolders). However, it feels like it takes a bit longer for the kobo to access each image, I also wouldn't put it past kobo to mess up sorting in that case as well.
An cbz-archive with hundreds to thousands of pictures works without flaw.