There is no Aikido without Atemi. that is of course if you practice Aikido as a Martial Art.
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.