Flying over a tropical storm normally doesn't present many problems except that there may be CBs building up or over your cruise level. These can normally be avoided in the usual manner. One other problem is that the air is usually much warmer over such a storm and that will limit your max altitude and in some cases mean you may have to descend a little if you are already at max altitude before overflying.
But the storm may render the airfields you may rely on as en route alternates unsuable, so that would be a good reason to avoid it.