I went to this cafe, it is at Toshima city in tokyo, and I asked the staff about this incident and a old man that was very nice seemed to remember. He was the manager and he said "that man continued to film even though we told him to stop", and "he was very persistent about filming so we told him to leave". I do not know whos lying or not but the old mans story sound more realistic, as he was very nice and offered me a free drink because my order was mistaken. This is a very lovely cafe and will allow you to film as long as you promise and mute or remove the music. Highly recommend it here.
If the new bills are the same physical size as the old, that's not a hard update. Coin vending is 100% based on the physical size of the coin so you can't update unless you replace the whole coin accepting internals. Huge difference between the two. But cash is kind of dying so that's not really a big issue.