Jessica,
Starting the Atkins diet won't have delayed your period, but changes in diet particularly as drastic as the Atkins diet can have effects on your body and potentially your cycle. My mom has been on the Atkins diet. While she has lost weight she seems a lot more fragile and forgetful. I'm not sure that the diet has been good for her, and I really worry about that. I'm not sure that the Atkins diet safe and healthy. I think it would be better to try to avoid processed white carbs and stick only to whole grains and less processed carbs - just my 2 cents.
I doubt that you are pregnant if you had several negative pregnancy tests. My guess is that for some reason your period is just irregular this month. If you are concerned you should probably see your doctor to have a blood test or to get checked out to find out if there is another reason why you are late. I don't want to advise you to lie to your husband. I suppose you could just go to the doctor without telling your husband, or could just tell him you have a routine gynological exam. It isn't advised to be on the Atkins diet or any fad diet if you are pregnant. Best wishes.
Kate