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If you created this epub with Sigil it will default to adding the nav.xhtml to the spine with linear="no" as its attribute.
The spine is a tag in the content.opf that lists the ids of the chapters in the order you want them to appear in the e-reader.
Have you tried validating your epub using the epubcheck plugin?
If you look at the content.opf, you should see the spine tag and inside it you should see an itemref tag with the idref="nav_xhtml" which is the manifest id for your nav.xhtml according to the snippet above.
When you say the nav TOC did not appear in Apple's Books app, are you referring to not seeing it like any other chapter, or that the Books TOC tool is empty?
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