Does the Roman god Mars exist? But we still have "martial" arts...
Science may not be able to prove the existence of ki or Mars, but that does not mean the the Japanese and the Romans respectively did not use these words to name some experiential reality. And that leads us to the question Ignatius asked: how can you practice Aikido, if you don't acknowledge the experiential reality of ki? Doesn't matter if ki has no scientific reality or if you prefer to use a different word of set of words to describe it, 'no ki, no aikido' still applies.
BTW, a more courageous (hence provocative) way to phrase your question would have been: Does God exist? But we still have Christianity...