Well. Actually, it all depends how you approach Aikido. There are ways of approaching it such that Atemi is essential. There are also ways of approaching it where atemi is almost incidental or even undesirable. They can both be martially effective. You have to have the knowledge and experience. Some do, some don't, some don't care.
There are real reasons why Atemi has it's limitations, under many circumstances - in fact, it can be your certain undoing if you're not careful.
There is no one way in Aikido that is the only effective way.
It is true that our opponent can over extend, which is what I understand ki no nogary is about. Like in swordsmaship, you can always cut the hands of someone that over extend and keep your self out of range.
So yes there is no need for atemi, in fact in that case it would be contra-productive
But there is case where our opponent does not extend outside his balanced extension range. In that case not using atemi is as contra-productive as using them in the case above