From the use of an erudite note on an illuminated manuscript to the modern footnote, marginalia have a very long history in their relation to the written word.
These marginal notes, almost asides, of course can contain extremely important material, and regularly point to other references that the particular work is citing in some manner.
Without the page a hypertext has no visible hierarchy that inevitably produces the relation of margin to centre that is the footnote. It allows for what is apparently minor to have an authority that is otherwise excluded, and also allows these parts of the text to develop their own links through a work.
Furthermore a hypertext can, in theory, link into the very work that the footnote otherwise merely indicates , in the process not so much softening the role of the marginal but dissolving it altogether. Here the relation between a principal text and the footnote disappears as the link performs an action that has the effect of producing an object that is neither one or the other, and privileges neither.