Nothing has changed and it has nothing to do with the iBooks app. eBook formats inherently use fluid page numbering since an eBook page is fluid - there is no fixed amount of text per page as it depends on the viewing settings and the device, hence page numbers inherently change. That is the very nature of an eBook format and it would be the same if that eBook was viewed in iBooks, Kindle, Nook, Kobo Reader or any eBook reader.
A PDF can be configured to have fixed page sizes and hence fixed page numbering, but eBooks (e.g. EPUB or IBOOK format files), by design, are fluid and adapt to the app and device. They would be horrible otherwise - imaging viewing a page on a 12.9" iPad Pro that had been formatted with a fixed page size format to fit on an iPad Mini display? Then you'd face the same limitations of PDFs and would have to zoom or shrink, and scroll up and down all the time to read them, instead of just turning the page like a..., well, a book.