Your title implies that hyphenation does not work at all in kepubs. My experience is that Dutch text in kepubs is not hyphenated according to the Dutch hyphenation rules that I supplied. In some more detail:
- without supplying a Dutch hyphenation file there is no hyphenation in epub or kepub;
- with a valid /usr/local/Kobo/hyphenDicts/hyph_nl.dic hyphenation works correctly in epub, but hyphens appear in arbitrary places, often incorrect, in kepub: uitg-esproken, ziekenh-uis, wasm-achine, tanda-rts;
- test cases have proper language code nl in dc:language element of opf and in xml:lang attribute on html element of xhtml;
- the presence of a symbolic link /usr/share/hyphen/hyph_nl_NL.dic does not seem to make a difference.