For what it's worth, you can have multi-level NCX on the Kindle, only it just displays the first level points in the location bar at the bottom.
In order to navigate the invisible 2nd level, you have to find a start point for said second level and flick back and forth to navigate it via the 5-way controller. It's enough of a hassle that it may be worth editing the original NCX to un-nest nested navPoints.
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