This topic was discussed in 2015: <https://lists.gnu.org/archive/html/emacs-orgmode/2015-02/msg00527.html>
However, it seems that it we are still stuck with inconsistent exports between latex and HTML. The issue is that when exporting equation numbers with ox-html, it uses MathJax's \eqref that wraps the equation in parentheses, for example: "Refer to (3) for more." However, when exporting the same document with ox-latex, it uses Latex's \ref that does not wrap the equation in parentheses. Would it be possible to add an option or variable to ox-html for the user to select whether to use \ref or \eqref on export? For those of us that publish to HTML and PDF, it is very difficult because you end up with either double or no parentheses. My proposed fix would be a change to ox-html from: (format "\\eqref{%s}" (org-export-get-reference destination info)) to (format (if org-html-export-mathjax-ref "\\ref{%s}" "\\eqref{%s}") (org-export-get-reference destination info)) The variable org-html-export-mathjax-ref is non-nil to use \ref vs. nil to be the default \eqref. Cheers, Brian