Some don't - they use the honor system. I think that's a reasonable choice depending on the spirit and intent of the hackathon. If your goal is to get a bunch of great people together to work on cool things, with a token contest prize and bragging rights, then worrying about cheaters probably isn't at the top of your "things to worry about" list.
If you do care about that, there are a couple ways you could structure the hackathon to eliminate some cheating (but a smart, talented, determined hacker probably can thwart them). Things like requiring submission of source code (then look at the git logs. what are the dates? are the first commits huge piles of work?) or structuring the contest around an unknown that gets revealed when it starts, like a theme (e.g. music-based apps).
