Yeah, that can happen. We typically use two atemis in Kote Gaeshi- One on the entry and one after the turn (whether it's a pivot or body change). I believe the rationale is that most people are going to recoil from a strong strike to the face, which begins the kuzushi. Another reason may be that it gives them something to think about while you are getting your wristlock firmed up.
I am a little confused about your description of dual atemi in kotegaeshi. I have two questions for you; which kotegaeshi variations are you using two atemi (please just list them via your dojo terminology), and do all your kotegeashi #2 involve an atemi before pivoting?