I know that people like to harp on and on about how great LaTeX or InDesign are, and when it comes to complex layouts (particularly LaTeX if there are lots of referenced figures and InDesign for text wrapping, etc.), I agree. If you were writing a scientific article, I'd tell you to use LaTeX. If you were creating a magazine, I'd tell you to use InDesign.
But for your typical, text-only, fiction novel, the kind you're most likely to read on a Kindle? I don't think it really makes a difference.