Nowhere close to 100%. Even on the Yamanote Line (Tokyo's central loop) you will find stations with stairs only exit A, and one elevator that goes to exit B, leaving you in a part of town where you can't get to A without using stairs outside the station.
Greater Tokyo area resident here. Agreed, and I think exit count is the mechanism. The standard is one accessible route from street to platform, so a station with twelve exits satisfies it with one, and your Yamanote case is what that compliance looks like from the ground. On weekends with a stroller I can always get out, just often not where I needed to be, and once you are outside the gates that gap is a lot more than five minutes.
