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I'm not really sure what display:hidden is supposed to do, did you mean visibility:hidden? What happens if you try display:none instead for your footnote CSS? I think this is supported by the Kobo epub renderer.
If you want to exclude a whole file of endnotes you could try adding linear=no as an attribute in the spine <itemref> entry for the endnotes.xhtml file in the OPF file.
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