Answers

My school did not offer a study hall, so I'm unsure of exactly what you're referring. Assuming it's a session for pure study during the day, I think that it probably has minimal effect on your application if it's a pretty typical class to have in your schedule. However, if you're looking into a top-tier school, why waste your time on a study hall session when you can be filling that gap with another higher-level class?

I think any top-tier college would respect a candidate who tries his/her best to take advantage of every educational opportunity.

At my school, no honors-level or higher students take study hall. If you're thinking about a top university, then you should avoid study hall.

If it's a common class to add to your schedule at your school, then you're probably fine. I don't think it should affect your app at all.