I agree that the "pages left in chapter" is very handy. I believe that a "chapter" is considered to be anything that is implemented in the epub as an H1 entry (in html terms). Such entries are also included in the Table of Contents. Sub-entries are implemented as H2, H3, etc. HTML tags. So, if the Nook uses the H1 entry as its mechanism to determine how many pages are left in a chapter, it will screw up if your epub has real chapters at a lower level (h2, etc) in that hierarchy.
You could reformat the pub with Sigil and change the real chapters to use H1 as the tag, but you'd have to remove that tag from the higher-levels (books). You could, I suppose, build your own links to those higher areas.
I am unsure about whether current Nooks show sub-entries in the Table of Contents. With the Classic Nook, they did for awhile, then they lost the ability, then I think I read that they have reacquired it. Keeps changing.
By the way, what does "ncx" stand for?