I suppose it could help some. The thing is, if those threads aren't being used, they don't really cause much heat anyway. It's when everything is being stressed that they can heat up your cpu, but that's also when they help it perform better.
For the most part, I would suggest leaving HT enabled. If you don't have good enough cooling for the worst case scenario, then you could leave them disabled and try overclocking some more. Generally HT can get good performance for its power use while overclocking that last little bit isn't so great.