Many authors, including me, would prefer footnotes, but commercial publishers won't use them for fear of scaring off readers. You're absolutely right about the website idea, however. I do have bibliographies on my site--publishers won't allow bibliographies at all--but at least some entries invevitably go bad, especially those from periodicals.

"commercial publishers won't use them for fear of scaring off readers"

You can always point those publishers to Susan Johnson's books. She writes best-selling, bona fide bodice rippers and gets to footnote historical explanations about condoms and underwear. The sex might be improbable, but all the other research is good!

The reluctance of publishers to allow footnotes is, I think, just as baseless as the magazine supersition about green covers. http://www.slate.com/id/2153949 An editor of my acquaintance admitted that there's really no evidence whatsoever that footnotes affect sales.

As for bibliographies, publishers' practices must differ -- I've seen lots of books, including trade books, that have bibliographies. Right beside me is Judith Rich Harris's "Nurture Assumption," which was published by Simon/Schuster, and has a 31 page bibliography.