iBooks iCloud Storage Limit?
I had this same problem - books added on my Macbook Pro stopped showing up on my iPad. I solved it by deselecting iBooks in iCloud on my Mac (System Preferences/iCloud/ ... click on Options tab beside iCloud Drive ... scroll down the list and deselect iBooks.app. If iBooks is open, a message should pop up that you can share books over the cloud, and it gives you the option to do that. Select that option. By deselecting and re-selecting in this way the books I was trying to share over the cloud immediately appeared on my iPad.