As a ride veterinarian, I see a few horses with heart murmurs every year.
Some of them do very well. In fact, I know at least one fairly top contender
that has one. As long as they have good recovery rates, I don't worry about
them. Just treat your horse normally and develop him to the best of his
ability, just like you would any other horse. Good thing you know about it,
though--always nice to know that it has been there for awhile and didn't just
develop all of a sudden. In my experience, sometimes they even get less
severe with conditioning.
Heidi Smith, DVM--Sagehill Arabians (Oregon)