The 9% is assuming that 100% of unknown cases are in fact negative.

This study showed that 110 of 111 players tested had CTE. But many of their families consented because they suspected CTE already, so it's not a random sample and therefore you can't generalize that to the rest of the population. 110 is 9% of the population of 1300 deceased players for the given time period. CTE is normally extremely rare.