I've no real experience in designing for books, but I do have some as a reader! I use a Kindle for most of my reading, so my opinions are more about ereaders.

I would suggest making labels a little larger than normal, as those can be hard to make out sometimes. And while we all like to make pretty maps with lots of detail here at the Guild, I feel you want the opposite in an ebook. Simple and clear works very well, even if it's not quite so nice to look at. Your idea of zoomed in maps is a good one.

I'd suggest making a somewhat stripped down version for the book, with a link to a more detailed version on your website. You can have best of both worlds that way.

Of course, the pros might have other opinions and suggestions, but that's my tuppence as a reader. Good luck with your book!