Thanks for the replies. The last two years we have done box squats that are above parallel and we also deadlift. So, we do get lifts with higher weight and a shorter ROM. At first I didn’t really push low squats because I thought being able to do more weight was more important than the benefits of going lower.
However, after reading some comments on this site and some articles about muscle activation I decided that low squats were better. The main reason was that deeper squats create greater activation in the glutes and hams. Also, it seemed like there would be benefits in hip and ankle flexibility.
So, would a mix of different depths work best? I was planning to do a combo of deep squats and more explosive box squats through a shorter range of motion.