What is the Difference?

Atemi (当身) means striking or concussive blows to the body... as opposed to grappling, throwing, felling or joint locking methods. Many Martial Arts styles employ the use of Atemi to help set up the opponent for a trow, lock or grappling action, but not necessarily the completion of a fight.

The striking to complete or end the conflict is more the line of Kyusho, where concussive strikes (but not limited to),  are used to dysfunction, incapacitate or kill the opponent.

Morehi Uesbia state that "Aikido is 80% Atemi".

This was not as much a focus of study, scientific or pragmatic, but more in line with an anecdotal method that served to emphasize O'Sensei's approach in explaining the importance of Atemi in Aikido.

It also follows along with what is known as the "Pareto Principle" in which; typically 80% of all problems can be resolved by 20% of all methods.  This is more of a natural law as opposed to just an Aikido principle.

Vast Population

This could also explain the reason for a large practitioner base in Kyusho being Aikido practitioners as well.

However that does not necessarily mean that Ueshiba, knew Kyusho.  Although given his time of developing the art, his background in Daitō-Ryū Aiki-Jūjutsu  under the styles founder Takeda Sōkaku... it was present.

The Jujutsu schools of that period did have Kyusho and the Healing methods of Kappo (活法) which are the resuscitation methods that involve the stimulation of specific vital points (Kyusho).  The term Kappo is a contraction of two Japanese words Katsu (resuscitation) and Ho (method) and refers to resuscitation techniques used to revive someone that had been choked to the point of unconsciousness, to lessen the pain of a strike to the groin, to help unlock a seized thoracic diaphragm, to stop a bleeding and other common training injuries (First Aid Methods). These techniques are also practiced by the martial arts such as Judo and Danzan Ryu.