A stuffy nose, though not life threatening, can be source of a lot of discomfort. There are a few possibilities for why she would still have symptoms, but to differentiate them requires a detailed history of her symptoms and a good physical exam. Only her doctor
(such as her primary care physician
) can formally diagnosed your wife and recommend treatment. Rhinitis is the official term for a stuffy nose. Chronically, it is caused by 1. Allergies, 2. Vasomotor activity, or 3. a side effect of medicines. Allergies are by far the most common. If your wife is taking an antihistamine, it is possible that she is not taking the best type for her, or that the benefit of the medicine is going away sometime in the middle of the night. This would especially be true if she takes medicine in the morning because the effects may be worn out by the late evening. Vasomotor rhinitis is a nerve reaction to a smell, dust, etc which causes the blood vessels to dilate. This type is may be more resistant to antiallergic medicines. Finally if she takes medicines such as pseudoephedrine or phenylephrine for rhinitis, withdrawal from these medicines results in worsening symptoms. As you can see, this seemingly simple condition is quite complex, and needs a formal evaluation before the cause can be sorted out. Good luck.