View the file names and directories of eBooks in iTunes
If your files are not in \iTunes Media\Books\ which is the default place to be when you tell iTunes to keep your media organized the they're in their original place.

How to know where that place is?


Go to books section in your library
Click the book you want
Get Info. You can right click or use your keyboard (control+I in Windows / command+I in Mac).
In the summary tab (first one loaded by default) you'll find a "Where" section at the bottom. with the path to the file.