you can't see it when you browse iCloud Drive in the Finder, a easy way to get to it:
Open any PDF; when it opens in Preview, right-click the titlebar and click "iBooks (iCloud)". When the iBooks finder window opens
drag the iBooks folder icon in the titlebar to your sidebar. now you have quick access to your ibooks.
You can now drag and drop books on that folder and they will be there when you open iBooks app.
In Mojave it appears it's no longer possible to drag the Books (formerly iBooks) folder icon to the sidebar. However with the folder open/frontmost (and with nothing inside the folder selected) selecting File > Add to Sidebar does the trick.
Or you can create a symbolic link in the home folder by running
ln -s ~/Library/Mobile\ Documents/iCloud\~com\~apple\~iBooks/Documents/ ~/iBooks