Splitting (not relevant for non-divisible elements), ctrl-dragging, and of course any client code that manipulates the document could end up copying nodes.
One idea I want to explore is to leave footnotes as inline content in the text. That might not be fore everyone (it requires a different kind of interface, and you won’t be able to have multiple paragraphs in a single footnote), but it’d be easy to edit. In this model, footnotes would just be an inline ‘style’ (I have to rename ‘style’ to something else, will do so soon – sorry about the backwards-incompatibility). But there will be awkwardness there too – we’d have to somehow prevent such pieces of text from being split.