Books App hiding Cloud books
The new Books App doesn't seem to have any method to hide books that are in the cloud. As with Music and Films I prefer to only see the items on the device when looking at my lists.
iPhone 7 Plus, iOS 10.0.2
One thing you can do is when in the Books app select Library at the bottom, select Collections, then Downloaded. From that option you will only see the books you have downloaded to the device.