Hmmm... I can see how being shy might be tough to swing into a positive light, but I feel like if it is something that clerkship evaluators have noticed, it might be on your dean's letter, in which case you definitely need to address it. Even if it's not in any of your letters, if it will be obvious in your interview (which is another situation in which being shy is a disadvantage) you might want to bring it up.
The rules our advisers gave us on the "negatives" questions was
1) If there is something negative in your file, use that. They presumably already know it's there (or will, once they read your app), and it will look strange if you don't address it. The interview is a time to present yourself in the most positive light, but also to stand up and explain the more negative aspects of your file in person (which, they did emphasize, is NOT the same as being defensive). Recognize the problems, admit them, show how you've grown, moved on...
2) You can be honest. Selectively honest, of course. What they really want to see is someone who recognizes that they are a human being, knows their faults, and has found some healthy, adult way in which to cope and move around those problems. it doesn't necessarily have to be a "positive" negative (like "I am too nice", or "I work too hard"), but it should be as benign a negative as possible and, in answering the question, you should display insight, problem-solving and coping skills... etc. I think the point of the question is more the process of how you deal with your shortcomings, than what exactly they are. Unless your weakness happens to be faking sick and/or lack of respect for authority. Then I might bend the truth a bit.
So, for specifics, if you think it's something that will be noticed, addressing it is probably the best course of action. But if you can't think of a way you've coped with it, etc, or any positive spin, maybe you can find another flaw to reveal...
