So the PT point of view on this is that bilateral breathing is better both for form and muscle balance. Unilateral breathing can cause shoulder pain, but it's related to roll. When you breath you roll farther (hopefully) so there is less stress to the shoulder on the breathing side. People tend to roll less to the non-breathing side and then strain their shoulder to get the hand out of the water for the recovery phase of the stroke. If you're a good swimmer and have a good roll to both sides, it's not bad to unilateral breathing. If you have problems with rolling, swimming even short distances unilaterally breathing can be bad.
Personally, I breath every 3 strokes when I race, 4 to 5 strokes when I'm swimming long endurance sets (3 makes me hyperventilate but if I'm swimming 4 I make a point of switching sides periodically), I often do sets to try to stretch my breathing out to every 7 strokes and when I'm swimming above my usual race pace I will often breath 3-2-3-2.
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