It's very irritating because it's the only way to refer to part of a long section. I'm going to have to start referring to paragraph numbers. Ugh.

Yes, exactly. Who cares that page numbers might canonically be for one paper size and not correspond to page sizes on some device? You can scroll or whatever and still use the canonical page numbers.

What's wrong with paragraph numbers? They are more precise.

Porque no los dos?

Since ebook readers can reflow text (after f.e. changing font size), page numbers lose most of their meaning.

Not so. Page breaks can still be rendered or marked anyways, and so can page numbers. And yeah, you're not going to see a whole "page" in one screenful, but so what?