Footnotes -- or endnotes, or just notes; whatever you want to call them -- are a problem. They're a problem for writers and a problem for readers and a problem for typesetters and a problem for page designers. But maybe we're getting closer to fixing that.
I'm old enough to remember the nightmare of trying to manage footnotes in a typewritten essay: they were easy to misnumber in the text -- you'd go 1, 2, 3, 5, 6 -- and easy to get out of sequence in the notes proper, so that the reference in footnote 8 actually belonged to footnote 9. You'd realize that you left out a citation, and would have to roll the paper back into the typewriter and add the number in the space between sentences, getting the superscription as accurately placed as possible, which was never very accurate, so the whole thing always looked sloppy. Then you'd have to type out your footnotes page all over again, and with all those underlines and weird Latin abbreviations (ibid., op. cit.) and publication details that had to be handled just so. You were sure to make more mistakes, especially as the hour grew later -- and then, alas, earlier.
And it's never been great for readers either. The easiest thing for writers and typesetters is to have all the notes at the end, but that can annoy readers. This particular problem goes back a long way. When the philosopher and historian David Hume read the first volume of Gibbon's Decline and Fall of the Roman Empire he loved the book but despised its endnotes. He and Gibbon shared a publisher, William Strahan, so Hume wrote to Strahan with a complaint: "One is also plagued with his Notes, according to the present Method of printing the Book: When a note is announced, you turn to the End of the Volume; and there you often find nothing but the Reference to an Authority: All these Authorities ought to be printed only at the Margin or the Bottom of the page." Each individual volume of the Decline and Fall was hefty -- as the Duke of Gloucester is reported to have said when presented with one, "Another damn'd thick, square book! Always, scribble, scribble, scribble! Eh! Mr. Gibbon?" -- and Hume was clearly irritated at investing the significant physical effort involved in turning to the end of the book only to find something like "Panegyr. Vet. vii.21." No fun in that.1