I just did a quick Google search, and it looks like Clerks 2's aspect ratio is 1.85:1. That's awfully close to 16:9 (1.78:1) and it wouldn't "shock" me if Apple (or the studio providing the Apple-compatible conversion to Apple) decided to crop the movie slightly so that it completely filled a 16:9 screen. Even though I consider myself a bit of an aspect-ratio "nazi" I personally wouldn't object much to having 1.85:1 movies cropped as 1.78:1.most recently clerks 2.
But I'm curious...did you notice significant black bars on your Handbrake rip? As I stated, that 1.85:1 movie is awfully close to the 16:9 (1.78:1) aspect ratio, so the size of the black bars should be pretty small, anyway. If you were seeing fairly large black bars, that would indicate that something was wrong.
Now, there are many many movies (possibly *most* movies) that are shot in a 2.35:1 aspect ratio. With these movies, the black bars will be much more noticeable, but I personally would be very displeased if Apple/whomever cropped those so as to completely fill a 16:9 TV, as you'd be missing out on left/right subject matter that the director intended you to see.