And the only time I've ever seen a Commander take control of a ship was in the absence of a Captain. Although it may be canon that Commanders can command ships, according to the various series anyway, they rarely do.

As for the numerous amounts of them aboard the Enterprise, I would venture three guesses.

1. They have a ton because they always have several high ranking officers on Away Missions, which could potentially result in heavily casualties. Thus requiring command staff at the helm of the ship.

2. The distinguished career of the Enterprise allowed these select officers to reach ranks they normally wouldn't have attained in the time period given.

3. More command staff makes for better tv