Yes, this is an issue on the Kindle device, but reading textbooks in the Kindle app on the iPad is gamechanging. The speed with which you make highlights, leave notes, and bookmark is great for learning. I can then access the book from my computer for quick reference and/or convert my booknotes to Anki flashcards.
This being said, I also own a Kindle Paperwhite and use it at least an hour a day for reading non-technical books. I can't recommend that device enough.