Yeah, it's just going to be unclear for a long time to come most likely.
If it's just for a class paper or something I'd just ask the professor who you should cite it.
If it's for something like a scholarly journal publication, I'd just e-mail the managing editor and ask how to deal with it since it's not going to be covered in the journals style guide most likely. They should either tell you how to cite it (or simply tell you to track down a copy of the physical book to get the paper page number).
Being an academic, that's one of many issues that keeps me from being interested in ebooks for academic works yet. I use ebooks pretty much soley for leisure reading, but will just buy/check out from the University Library any academic books related to my research/publications.
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