Have you declared the namespace prefix epub
to lxml?
>>> tree.getroot().xpath(
... "//li[@epub:type = 'footnote']",
... namespaces={'epub':'http://www.idpf.org/2007/ops'}
... )
Update per question update
The XHTML namespace is also tripping you up. Try:
>>> tree.getroot().xpath(
... "//xhtml:li[@epub:type = 'footnote']",
... namespaces={'epub':'http://www.idpf.org/2007/ops', 'xhtml': 'http://www.w3.org/1999/xhtml'}
... )