Clever idea in general, a few issues:
1. Sometimes people upvote without reading the article just because the comments are good, and want others to benefit from that as well.
2. Sometimes people upvote to save a submission, since there's no separate save function. For example, I want to send it to a friend later, but not right now, so I upvote it to make it easier to find (b/c HN search is hit-or-miss).
I confess I'm guilty of these, but I doubt I'm the only one.
By way of comparison, take Reddit. Upvoting and saving are separate functions. You can save submissions you think you might want to revisit later. Reasons for doing so:
1. Scanning the headlines quickly, but don't have time to actually read everything, want to save the article and comments for later perusal (lunch break, after work, whatever).
2. Subreddits reduce the cost of upvoting. For example, every time I consider whether to upvote a Bitcoin story on HN, I consider whether it's front-page worthy. On Reddit, that's not a problem, I can just assume it won't hit the general front page b/c it's a relatively niche subject, but the upvote might help it within its own subreddit.
One more potential problem with the idea of superflaggers. If 'social media experts', or spammers, or whatever the people are who game sites like Digg and Reddit got wind of the fact that flagging honeypots could increase the weight of their flags and/or votes, mightn't they also figure out how to abuse that?
A professional, as some of them seem to be (eg, able to spend all day every day doing this), might be able to achieve a denominator very close to 1, and a numerator close to the total actual honeypots.