I voted "almost always".
I don't teach much this way, and don't necessarily agree with it. However, it does seem to be the fastest and surest way to teach students to protect themselves.
There are plenty of techniques where uke's response to an atemi leads into the technique. If uke doesn't deflect or avoid the atemi, the technique becomes much shorter (for example, katadori ikkyo). Without a sincere atemi ( =sincere block by uke ), the whole logic of the technique falls apart.