well, i have designed a number of books (i think my biggest was about 450 pages) and unless i am missing something (which is certainly possible) i have always done it in indesign.
i setup my H+J's in ID but at the end of the day i am manually looking at every spread and every page and making sure to check for widows, rags, spacing, etc. i would never, ever trust a computer to do that beyond initial flowing of text into columns.
i know there is Framemaker which i have never used, tho my understanding is that is more for working with XML and data-merging stuff rather than just straight layout.