@koland,
After years of use and a couple thousand books, my thumbnails have grown to a whole 32 MB -- 1/100 of the total space on my Kindle!
Annotations are miniscule.
When deleting a book:
Assuming the book is not from the Kindle Store, all it saves is highlights/notes/bookmarks/current page. It never had the other data (which I still don't believe is as much as you say, though I cannot confirm goodreads data) to begin with.
If the book
is from the Kindle store, nothing at all is saved.
Search Indexes track the books you have currently on your device, and they are a feature many people desire.
My search indexes use up 1/4 again of the amount of space my documents folder does. That is a sacrifice most people are willing to pay. If not, see:
Kindle_Touch_Hacking#Search_Bar_Shortcuts and disable the indexer.
P.S. "Well over the size of the book itself, in most cases." You must be quite special. I haven't ever seen that at all, and I haven't heard of anyone else with your problem either.