Not a cardiologist, but a physiologist.
Cardiac hypertrophy due to exercise should not cause an ST segment depression. It will change the electrical axis of the heart more toward the left since the left ventricle is undergoing more hypertrophy than the right from long-term endurance exercise. This would show in the V1-V6 single leads and the QRS will be larger in the Lead I vs. Lead II.
I'm going off the top of my head here without my EKG interpretation book around, but ST segment depression USUALLY indicates mild ischemia or ischemic damage of the myocardium.
T waves themselves are a bit funny. By that I mean, usually T waves deviate upward like P waves and the R of the QRS complex. However, some people have biphasic T waves and others even have T waves that deviate downward. My dad's does this and EVERY other variable indicates he is perfectly healthy.
So, what lead were you looking at? The "standard" that most people see is a Lead II. When EKGs are shown in movies of patients, you are almost always seeing a Lead II. Usually, the T wave on Lead II should be upward deviating, but again, see above.
So, I'm wondering if you may have a biphasic T wave that is appearing as a depression of the ST segment. Of course, this is no diagnosis, and you should go back to your Dr. But worrying about it at this point, is, in my very humble opinion, not worth it based on the other information you've given.
I'll see if I can find my EKG interpretation book and give you a little more.