Practically, numbering equations works, sequenced in the article from beginning to end. While it is a courtesy to readers and arbiters, later, who discuss lines that the author did not, it most certainly adds specificity, without tortuous sentence structure or word choice. "Equation 24" will always be just that, regardless of its placement on the page, and regardless of reprint formulation or quality.
As as an editor, my choice is to number all equations, and bold those that are referred to in by the text of the article.
Equation identification, when there is textual sectioning, by chapter or other means, can include the section as predicate: e.g.: 5-24 is refers to equation 24 in chapter 5. Texts that use this system (or any system) wisely place an explanation at the forward.
Obviously, longer papers/articles, or complex sectioning, both complicate the system for the reader, the ultimate consumer for the publication (e.g.: 5.3-24). Personally I would avoid it; I can't imagine the necessity of referring to large counts of equations in other chapters or sections, and in those rare cases, for a reference such as "see equation 5-24", I would consider adding a postscript: "in Chapter 5.3" or "at page 137".
