Glad that your son is better (no more head tilt or breath-holding). Unfortunately, I'm not quite sure where the cyst is by your report or what kind of cyst it is (very important to know exactly where it is in relation to the brain - in/outside, over the covering?, etc). Many times, when we do an MRI of the brain we see what's called incidental findings. This means there is something in or around the brain that really does not have any clinical significance such as an arachnoid cyst. If this is what your doc is talking about, then for the most part it's true. The arachnoid cyst is a pocket of cerebrospinal fluid that in many cases does not have any clinical significance. Many of them remain that way for life, but some do grow causing neurological problems depending on where they are. It can cause seizures if near the surface of the brain and it can cause weakness/sensory changes of an arm/leg, both again, depending on where they are.
Stay in touch with your peds neurologist. As long as your son continues to grow and develop normally and is the "bright and normal child" you describe, then it is likely that the cyst was just an incidental finding and that his headaches were just migraines or somthing that was transient and not serious. I agree with the followup MRI in 6 months. If your son develops any problems or worsening/recurrence of headaches, don't hesitate to bring him back to the neuro ASAP> Best o luck,.