It doesn't sound like he checked for any scapular positioning/scapulo-humeral rhythm which I think is a big piece of the puzzle. Obviously I don't know who your doctor is as I don't know you or the doctor's name and I am in no way trying to discredit your doctor's intelligence or medical capabilities.
(Brief step up onto soap box) I think this is an example of how the insurance companies and corporate aspect of orthopedic clinics push for doctors to see more and more patients in a short time span, so they don't have the time to do as thorough of an evaluation that they should do (step off the soap box).
Without doing a physical eval, here are some general things that could be going on:
-Structurally you may have a hooked acromion that may cause an decrease is space and increased change of impingement.
-There may be some capsular tightness causing GH shifting
-Poor thoracic mobility
-Poor scapular positioning and scapulo-humeral rhythm.
-Tight anterior muscles (pec major, pec minor, subclavious, etc)
-Weak posterior muscles (rhomboids, lower trap, middle trap, etc)
GENERALLY, if the clicking doesn't cause pain it is not a major cause for concern, but does show that you probably have some mobility restrictions that could be addressed. Other people you can look into are to try and find a more thorough sports medicine orthopedic physician (do some research before going to see one), find an athletic trainer or physical therapist who works with a lot of athletes (again, research), or a functional movement specialist (could be an AT, PT, strength/performance coach, or other professional). Z-Health has a very thorough movement screening process so if you can find one of their practitioners in your area, that would be a good option as well.