I just find it strange to think Nishio Sensei would dedicate so much of his life to Aikido if he really believed 99% of it was ineffective. Nishio Sensei obviously is concerned about Aikido retaining its martial integrity as an art and has sought to augment this by becoming a student of other forms of budo. However, he could easily have chosen to give up Aikido in favour of another martial art that he saw as more effective.
Maybe he just found the ideals and teachings of Ueshiba to be more important than waza? Maybe the paradox of non-violence and martial integrity was as faschinating to him as it is to so many others?