>"Isn’t it? Every page of the Talmud includes marginal notes (Masoret HaShas, Ein Mishpat, Torah Or) giving cross-references to relevant parts of the Torah, Talmud and other legal codes. In a web-based version I think it would be natural to represent those with hypertext."

True, and the website "Al Hatorah" indeed does that, for the marginal notes that you list. See, for example: https://shas.alhatorah.org/Gemara/Berakhot/2a

But my point is that those marginal notes are an artifact of the 16th century print edition. It's not anything inherent in the Talmud text.

The famous 16th-century Mikraot Gedolot edition of the Bible also features extensive marginal notes (the Mesorah) which function much like a dense network of cross-references.

In fact, the Mesorah is a medieval work (drawing on ancient sources) and is arguably was one of the most elaborate systems of cross-referencing found anywhere, at the time it was promulgated.

This differs from the Talmud’s cross-referencing, which doesn't predate the printed edition (as I note in the Seforim Blog article; the page citations are reliant on the universal page numbers that started from the first print edition).