I must respectfully disagree, Sil_liS. When quoting, etc. in academics, it is always by page number. It is the world-wide accepted format for quoting books, magazines and journals. That is the reason the publishing information is so vital (and also why full URLs are required for websites, as well as the "date" of "download"). If I quote from a book in my work, just giving a section title does not "cut the cake". I STILL have to find a hard copy page reference.
In addition, academic writing is not necessarily broken into small sections--that is neither good nor bad and has to do with many factors including writing culture (I teach research writing in different languages and am a technical/academic/medical translator). It is not provided for by i.e. MLA or APA or any other academic structure. In fact, overly using paragraph titles (overly short sections) instead of transitional phrases is considered "bad form" in many fields.
And as has been noted: different pages, etc. for different formatting means it IS harder to find a quote in a chapter extending 10-15 pages without a page reference. That is why often-times in courses specific books complete with ISBN are "recommended" in the syllabus.
I believe that this is the reason some readers here want to see book pages and notice them missing, whereas others don't really bother or even prefer the % bar. It has partially to do with what your reading is primarily for.
For leisure, page numbers are not so necessary. I, too, "thumb to a page" by percent on a pbb. For academic reading (or even for a book club), a universal "page number" restricts the "scan" field for those following the lecture and can be very beneficial.
If there were a solution (pdfing is one of them, but not perfectly implemented), it would greatly push ebooks into the academic fields. (i.e. "invisible page numbers" to jump to according to the book edition.) Unfortunately, I am not capable of implementing such a background/invisible structure including reflow to make it pretty--I can only hypothesize.
