Hi Hans, your mother has nothing to worry about. Both the trains and the train stations are fully equipped with wheelchair accesable tools such as ramps for the trains and elevators in the train stations.
When you arrive at the train station, the JR staff will most likely ask if she need any help and get her to a certain waiting area and help board the train once it arrives. However, if your mother rather go by yourself, the staff will come and help her board the train once the train arrives at the platform.
With kind regards, Jonathan H.