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To address your point about the epub2 "still having the toc.ncx file:" it should.
As Kevin mentioned, I'd keep using the validation plugins to see what needs attention to make your epub v2-compliant. I've no idea what kind of EPUB3 InDesign creates, so I don't know how much work that will require.
Not really sure why you'd want to remove the nav.xhtml from the epub3--or the toc.ncx from the epub2, for that matter. They're both expected/used in the Kindle conversion process (as well as being required by their respective epub version specs)
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