Ideas: use scribble numberers (http://docs.racket-lang.org/scribble/core.html#%28tech._numberer%29) or MathJax's automatic equation numbering http://docs.mathjax.org/en/latest/tex.html#automatic-equation-numbering .

Using scribble, the numbers would form a single sequence across multiple HTML files when a document is rendered as separate files (and references should be easy enough to implement). With MathJax's solution, we would get an output closer to LaTeX's in HTML mode, but references across separate HTML files will likely not work properly (even if all files come from the same .scrbl file).