EDIT: I don't ask about the difference of meanings, there was this question a while ago that states the difference, as @Ankur Banerjee underlined it.
This has annoyed me too.
I think they're different because different people made them and only moderators can change them.
I just had a quick look with Google's N-gram tool and it seems the single-word version is the most popular in each case:
Maybe retain hyphenated versions as synonyms too, that never hurts.
Because layovers and stopovers mean different things. Not that I'm sure people generally know what the difference is, and thus use it interchangeably. Perhaps we should merge it. I'd say merge with layovers as main tag.