Pandoc does provide a way to link to section headings, but it doesn't yet have a generic system for autogenerating numbers and producing references to these, like LaTeX's \label{} and \ref{}. It does, however, have a system for creating running example lists: http://johnmacfarlane.net/pandoc/README.html#numbered-exampl.... This can be used for numbering equations and referring back to them, but it is considerably less flexible than LaTeX.
Pandoc has extensive support for automatic citations using CSL stylesheets: http://johnmacfarlane.net/pandoc/README.html#citations. BibTeX and BibLaTeX files can be used as the database, or YAML citations can be included in the markdown document itself.
LaTeX formulas can be embedded in markdown. They can even use macros defined in the document. Formulas can be converted to MathML or native Word equation objects, depending on the output format.
Pandoc can also be extended using "filters" that operate directly on the parsed AST. Here's an example of a filter that finds tikz diagrams and converts them to embedded images that can be displayed on the web: https://github.com/jgm/pandocfilters/blob/master/examples/ti....