I you're already using KUAL take a look at
this KUAL extension for deleting those .sdr folders.
Also, I thought that deleting books with Calibre deleted the .sdr folder? Or is is only deleting .mpb and other files inside the .sdr folder but not the folder itself (living an empty folder?)??
I remember only that deleting the book via Kindle's GUI doesn't remove associated .sdr folder (files inside nor the folder itself)...
I delete books mainly via Kindle itself and periodically use that KUAL button to clean up the leftovers.