(1) How is publishing different for nonfiction children's books? (For example, a science topic for middle grades)It's SO different! It's furrier, for one thing, and sometimes it's purple!
Ok, so I didn't really understand the question. There aren't a lot of differences, aside from submission (see below) and the need for fact-checking. Were you thinking of something else?
(2) I know for adult nonfiction, authors are not expected to write the whole book before submitting. Is that true of children's books as well or do editors expect the complete manuscript?
If it's chapter-length nonfiction, then yes, usually those are sold based on sample chapters and an outline.
(3) Are nonfiction titles a harder sell to publishers/bookstores?They certainly can be. Some nonfiction sells great---The Dangerous Book for Boys, for example. But a lot of nonfiction (especially chapter-length nonfiction) only does well if it's very well supported by teachers and librarians, and as you may have heard in the news, they have NO MONEY TO SPEND ON BOOKS right now. But that's ok, because we didn't want those kids educated anyway. Who cares if they'll be old enough to vote soon? Most adult Americans NOW don't know what "nonfiction" means, and everything's just fine, right?