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There is nothing hidden about the footnotes page. It is the aside element that would need to be hidden. And in fact, even if calibre output epub 3, footnotes would not be put in aside elements as that is just less broadly compatible and offers no actual benefits.
About the only thing that would change when outputting for epub3 is the footnotes would have the added epub 3 specific epub:type annotation -- which is really not required for any halfway decent epub reading software. Detecting footnotes using heuristics works great in most readers.
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