I believe most ID's and passports to not allow for hyphens-- I could be wrong, though.
In any event, it is pretty obvious that you would just put in the name without the hyphen and let it clump together.
Well, they use the term 'exactly'. A person named John Doe-Smythe is not the same as John DoeSmythe. Remember that we're dealing with both the airlines and TSA. If it can be screwed up resulting in a passenger not flying then between those two they will move both heaven and earth to do so.