This may be an indication of joint laxity or a developmental problem, or it may be unremarkable. Have you ever cracked your knuckles? The source of that sound is the sudden release of air bubbles in a joint space. No harm in the cracking sound, but it can be dramatic.
If there is any lameness in your puppy or reluctance to walk/play/run/jump then have her examined and possibly radiographed (x-rays) to see if there is an underlying cause for the clicking noises.
At the very least I would make certain that you are feeding an adult diet to such a large puppy, avoid puppy chow in large and giant breeds after four months of age. Slower growth reduces developmental problems, and the puppy will reach normal size within the two-year mark.
Dr. Van Lienden
Dr. Raymond Van Lienden DVM
The Animal Clinic of Clifton
12702 Chapel Road, Clifton
Virginia, U.S.A. 20124