In a highly trained athlete with eccentric hypertrophy of both ventricles, what is the significance of a high ejection fraction (80%) and high fractional shortening (50%)? cardiac output is also high, cardiac index at 6.4 or so?

Depends on whether the study was performed at rest or during exercise. The ejection fraction is usually lower at rest , but may increase during vigorous exercise. A cardiac index of 6.4 , if recorded at rest is much greater than usual unless there is significant bradycardia which may occur in athletes at rest. More detail (resting heart rate, heart size etc) would help to interpret better.