booksitunespdf
There are several PDF files which I imported into iTunes to read using iBooks.
However, I cannot manage to remove them. By default, iTunes handles the its media library automatically. The PDFs and iBooks are stored in:
~/Music/iTunes/iTunes\ Media/Books/
When I remove the PDF files here, they will still show up in iTunes.
How I remove their entries in iTunes?
What you call a “design” flaw, is not such thing. It’s a design decision made by the iTunes team. Although iTunes lets you “manually manage your library”, it’s never intended to let you move things around in the filesystem, add, remove or modify files.
The premise for iTunes happiness is that you always add the items to the library and modify things from within iTunes. You have the choice to let iTunes “organize” the library (which will copy the media to the iTunes library folder and organize it there as he wants) or you can leave it wherever you originally had it, but iTunes doesn’t “read” or “monitor" the filesystem for changes. It knows things changed when the library.xml is changed, and the only application that does that is iTunes itself.
Is this the best way?
Yes and no, it has advantages, but a lot of people miss the “Winamp-like” ease of use and it’s understandable. On the other hand, it simplifies a lot of things for a lot of people. It has decently worked for quite a few years now.
But that’s the topic for another discussion. :)
On a Mac: Drag the files into iTunes with the option key down and the files won't be copied to your iTunes Media folder.
That's the exact result you like.
There is also the option to change it so you don't have to press option key: 
You can press option key after changing that setting to copy it on purpose. (Exact opposite of default setting)
Good luck :)
Best Answer
Can you not select the book and use Command ⌘ + Delete ⌫? You'll be presented with a choice to delete the book from the library, or move it to the trash:
You'll probably want to move it to the trash, unless it's a PDF that you don't have somewhere else. Also, make sure that you are going to the books tab on your computer, not managing the books on your device.
Here:
Not here: