two things. first a ct scan is the definitive test for sinusitis. if it was clear then i would question that he is having "sinus headaches". there are a hundreds of different types of headaches so consider seeing a neurologist for a higher-level evaluation. second taking decongestants at night is not a good idea because of their stimulent effect and the fact they cause annoying drainage. an antihistamine may be considered or perhaps a trial of using nasal corticosteroid sprays to reduce the inflammation.
my husband has sinus headaches that wake him up every night. decongestents don't help and ct scan showed nothing. he will often take steam showers to break up the congestion in his head then have to sit up for 2 or 3 hours for his head to drain enough to go back to bed.