I was a very active member of the HH community and part of the team that hosted DubHacks (
http://dubhacks.co)). Personally, I've attended over 15 hackathons in the last two years, but recently stopped because I share some of your concerns.
1. After going to a few hackathons, most of my side projects had very "hacky" code - not something I liked and definitely something that goes against the basic SE practices.
2. Most hackathons don't challenge participants to innovate, but just to "make something cool". I have seen a few truly innovative projects being made in only a weekend at hackathons that did not get enough attention let alone a prize just because they weren't cool enough.
3. There have been numerous hackathons where winning teams made something so stupid, it filled me with rage (eg: http://hackgt2014.challengepost.com/submissions)
4. The Facebook group has essentially become a circlejerk - it had a lot of value when there were 5. Too much focus has been on horizontal growth and not vertical - how many students can we get, how much sponsorship, how much food, how many Medium posts. A lot of of deep thought is missed out.
But at the end of the day, I think hackathons have their own place in helping schools become more progressive and to give students exposure that's left out of the classroom. I also think the best hackathons are the ones that motivate new comers to try something new and to give life to their ideas with resources and mentorship. The focus of hackathons, IMO, should be on learning and networking rather than winning. It'd be nice to have a very personalized hackathon experience now for a change.