The discolourations don't bother me too much - except when they cut across an important line. There's no predicting them, they're like a mild practical joke played by wood.
Proper knots and shakes are a different matter and an irritation. But like hurricanes and diarrhoea, they're a natural and largely unpredictable force of nature, and there's not much to be gained from fretting over them. Hard beeswax can work wonders.