Nobody knew the 1966 storm would be so intense
First, the 2001 storm was very, very intense. Not as strong as the 1966 storm at its peak, but since that peak ocurred over such a small area, it's quite possible that ISS got hit just as much as a capsule would have in 1966.
More importantly, we were not good at predicting meteor storms back then. There was suspicion, certainly, that there would be something happening, but no one knew it would be 100,000 visible meteors/hour, nor the exact time/location of the peak
