Yes, it was real, and it worked like you were in the middle of the clock's face with twelve directly in front of you and six directly behind. The reference to High or Low were and indication of the enemy aircraft's altitude in comparison to the aircraft you were in.
So Twelve O'clock High means the enemy was directly in front and above you. Answer This was especially useful for crewmembers on board a B-17 or other heavy bomber such as seen on 12 O'clock High. There were 6 or 7 gun positions on a B-17. If a gunner saw a enemy a/c and called out "Enemy A/c to my right", no one would know who said it nor which direction he was looking. They need a reference system. By using the Clock technique, they could call out out an enemy threat with reference to the a/c and everyone who heard it would automatically know which direction to look with respect to their position. This is still used today in the age of fighter jets. "Check 6" is a common term among fighter pilots that means always watch your rear and is used as a salutation among pilots.
BTW, in the bomber pilot jargon, "EA" was short for "enemy aircraft" and was used quite often in the after-action reports.