I can't speak to whether the Kindle editions are better formatted technically or not; all I can tell you is that the Nook editions I've bought of the two most recent Trek books have been formatted properly, and that I'm very pleased with my Nook (not the least because it helps prop up a book-selling business that isn't named Amazon.com).
There's pretty much three distinct generations of eBooks from S&S:
1) 1979 - ~2000: Older titles that were scanned/OCR'd. These aren't going to look particularly good on any platform, and are going to be the prone to errors.
2) ~2000 - ~2009: Titles with electronic sources that were released for MS Reader, Mobipocket, and Palm eReader. These should have clean text on both Kindle and ePub, but the ePub version is likely going to have formatting errors (it looks like S&S converted the ePubs from another format rather than recreating them from the digital source files) that won't be present in the Kindle version (since Kindle is
3) ~2009 - now: Titles with electronic sources that were released for Kindle and ePub. These should have clean text and formatting on both platforms, but the ePub will look nicer (thanks to the custom fonts and better formatting).