What is the standard way to refer to shared code in conference papers?
I have seen all of 1-3 in papers. I would favor a link in the text or footnotes over a link in the references, to underline that the code is part of the contribution of the paper. (If it isn't, e.g. because it was already presented in one of your previous papers, or because someone not on the authors list wrote a significant portion of the code, put it in the references instead.)

Definitely mention the link in the paper itself, so that readers of the paper can look it up. Also, for convenience, it's nice if the URL is a clickable link in the PDF.