I've narrowed the problem down to https://bazaar.launchpad.net/~unity- team/unity/trunk/view/head:/unity-shared/GnomeFileManager.cpp#L216. Calling GnomeFileManager::Activate() from GnomeFileManager::EmptyTrash() seems to no longer be necessary and causes Nautilus to open a window at the user's home directory. Simpy removing the function call from my copy of the unity sources fixes the problem with no side-effects as far as I can tell.
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