I have the same problem with gigantic margins on many ePub files I've used through ADE. I can't fix these in Calibre because I have no idea how to remove DRM. It's a shame, because this would be an easy solution to the big formatting problem: the space between paragraphs, and the lack of a first-line indent.
RE: justification -- Physical books have justified text because it's a more elegant and readable way of designing a book. It simply LOOKS better, but also the eye is thrown by ragged-right text (even if we're not conscious of this happening).
But on a small screen like an eInk screen, justification has the exact opposite effect. It looks worse and is less readable because of the gaping holes and rivers created in the text.