Originally Posted by Doitsu
KindleGen does not ignore the .ncx file; the .ncx file is included in the .mobi file and can be used instead of the inline TOC for chapter navigation with eInk Kindles that support firmware 5.1 or higher (e.g. Kindle Touch). Even K3s support rudimentary .ncx navigation: users can select previous and next chapters with the 5-way button.
The NCX is not converted to a ToC in Mobi. So when you use Kindlegen to convert an ePub with only an NCX ToC, the Mobi ends up with no ToC. That's what I mean by ignores the NCX.