There is no way to ignore the NAV when using the auto Create Index feature (nor is there a way to ignore the copyright page, or the half-title, or the epigraph, or the dedication, etc...). You can, of course, edit the index to remove any entries you don't want after creating it (or manually create the index with exactly the item you want). It's not an unreasonable request to be able to ignore files in the auto-creation process, though. We'll look into it.
As for the second request: as far as I'm concerned, you've just been handed one more reason why littering an ebook's text with soft-hyphens is a terrible idea for ebook creators.
