Because the math has nothing to do with the total amount of points given out. There is no defined total amount of points that can be given out in an NHL season.
The equation is very simple. P% = (# of points a team earned)/(total # of points a team could heave earned).
Just because 3 points were given out, it doesn't change the fact that the total # of points a team could have earned from a game was 2 points. The denominator goes up by 2 every game, no matter whether it finished in regulatin or went to OT...
You're operating under the assumption that P% must average out to 0.500. That's not the case because the number of points that can be given out is not static.
Doesn't that sound wrong?
Let's propose 2 scenarios with 4 teams each playing 82 games.
Team A plays Team B 82 times.
Team A wins 5 games.
Team B wins 5 games.
Team B wins 72 games in overtime.
Team A's record is as follows: 5 -5 -72
Team B's record is as follows: 77 - 5 - 0
Team A receives 82 points.
Team B receives 154 points.
According to your equation, Team A has a .500 record.
Team B's record is .940
Now, Team C and Team D play each other 82 times as well.
They split their season evenly at 41-41-0 each.
Both teams end up with 82 points.
Both teams are .500