Do not skip seeing Sainte Chapelle if you are in Paris. It is simply gorgeous and will not take a massive amount of time to go through either. As for the skip the line tickets, they're probably not needed. We went in the middle of the afternoon and the tickets saved us likely 5-10 minutes in line. If that's too long to wait, you can go early in the day and not worry about any wait.
Saint Chapelle was a visual treat! We are happy we made time to visit the chapel. However, I felt that one need not book skip the line tickets in advance. The queue was not at all long if you an manage to be there in the morning. We were there around 10am in July, the peak tourist season and it was just us a couple of other small groups.