This is still practiced if the home buyer requests it when the home is built and is willing to pay the price difference. It makes a better roof surface even though the knots will fall out. If I built a house I would definately look into the cost of 1x6 decking rather than that crap OSB plywood. Most of the knots are no bigger than golf ball diameter and it will not compromise the roof surface unless a hailstone finds that spot. My parrents live in a house thats 50 years old with this type of deck and the same thing you describe has happened to there roof with no issues.