For what it's worth, with regard to the hypenation thing I've been doing with my previous (and in-progress) books, in doing it the way I outlined, and testing it out on the iPad in
all font sizes, both in portrait and landscape orientation, everything turned out remarkably well, way better than just leaving things to the "default" (i.e. by having not done what I did at all). Not only is the text more visually/aesthetically pleasing to look at, without a zillion needless hyphenations all over the place, but there's not a single instance of "large white spaces" anywhere, and hence, as a result of all that, not only is the book more visually "pleasurable" just too look at (from a design perspective) but overall ease-of-readability is improved, too (because there's fewer hyphenated words all over the place).
I can appreciate both your concerns --
if what you're concerned about was actually happening -- but in fact the exact opposite of what you're concerned about is the end result of doing what I did.