Where did she download it from, and what does that site say about it being stored in the cloud? I download from Amazon (Kindle format) all the time and the books are not stored in the cloud.
If she has an automatic backup, it MIGHT be keeping a copy in the cloud even if she deletes it from the phone. You will have to delve into the mysteries of Iphone syncing to figure that one out.
Ebooks are NOT big files, and she would need THOUSANDS of them to consume any significant space in cloud storage. Not something you need to worry about, really.