I use a blank paragraph for scene breaks because when I use margin-top, mobi7 doesn't honor it when I convert it via kindlegen (the new mobi seems fine). The blank paragraph with a non-breaking space is honored on every reading device I've looked at. I know it's bad code, but fortunately, nobody is looking at my code.
That said, why not add the non-breaking space in InDesign? It's on the Type menu under Insert White Space (or memorize the keyboard command).