It's mainly because a majority of the time we have gusty winds, they come from the south. The barrier the bridge forms also helps to churn up the water somewhat on the windy side. In the meantime, the bridge blocks the wind along the north side, leaving it eerily calm.
However, there are times when we have a strong arctic wind event that it can be reversed, and the choppy water is on the north side.
The DOT says they would open the 520 bridge's drawspan if sustained winds reach 50 mph for 15 minutes.