No, not a stupid question at all.
While experience and clue-specific techniques, like you said, are significant factors, there are also some tricks. One that comes to mind is that you can submit your answer as soon as you fill in green circles for the first set of rows (all the way across). In other words, crossing off false combinations (anywhere) and adding circles for the lower parts of the grid only needs to be done to the extent that it helps you figure out the true combinations for the first set of rows. I too was nowhere near average when I started, and though experience allowed me to get much closer to average, I don't think I've ever got better than average when I fill in the whole grid. (Even using this I can't get much better than average, though.)
As for the unbelievably fast times, I think many of those are done using some amount of pattern recognition. Basically, although the site randomizes names (I think), there are a limited number of puzzles that are truly different, and some people play so much and have such a good memory that they can recognize which puzzle they are doing part way through and just fill the rest in from memory. The site creator mentioned that, although pattern recognition isn't exactly cheating, the next major update will probably include changes intended to prevent it.