Are allergies worse in the morning?

Very likely. Hay fever/allergic rhinitis/nasal allergies are usually due to pollen allergies and most plants pollenate in the early morning. Also, inflammatory processes tend to peak between 2 to 4 am so asthma, involving inflammation of the bronchial tubes, tends to be worse at that time.
Yes. Your immune system is toned down along with many of the bodies functions when you are asleep. When you wake up they suddenly go into active mode kick start the allergy symptoms when you start your day. If you have indoor allergens like dust mite or pet dander they can be worse.