You put line numbers in the margin (with css styling), or I've also seen it as [#] inline in the text, possibly styled differently to make it more intuitive that it's not part of the source text.

For the vast majority of works that are untranslated, that isn't necessary, because, as mentioned, search works fine, and it's faster, too. For translated works, the concept of one published source of truth for page numbers is already broken, so you need some alternative to page numbers anyway.