I am the adoptive mom of two children (now ages 21 and 14) with shunts for hydracephalus. Although this is quite different from your diagnosis, I imagine the shunt would be similar, and it would certainly not cause any problems with the wearing of a helmet for riding.
In fact, some children with shunts wear helmets at play to protect the shunt placement.
Our son has ridden successfully in a therapeutic riding program.
Each has a number of complicated medical issues in addition to needing to be shunted, but for us those shunts are a wonderful blessing and are what keeps the kids healthy and functioning.
You can feel them with your fingertips in the hair, but cannot see them. The docs at OHSU in Portland, Or, do not even shave the head. In a few days, you wouldn't know they procedure had taken place.