I am a big fan of Tufte's work and try to employ my understanding of it when possible. I've never really had a criticism that seemed worthwhile. Even this page - I read to the end and thought this is fantastic.
However, perhaps because I only skimmed the page contents, I struggled to find the link to the github project.
Wonder if that is my brain being conditioned by expectations of a "normal" webpage or that the links have to be highlighted differently.
PS: I do not recall if Tufte's work addresses hyper-links explicitly.