I.G.
If you haven't done so yet, a trip to the pediatrician would be in order to exclude any more serious health problems.
If they don't have an underlying condition it might just be that their airways get dried out from either air-conditioning or having a fan running in the bedroom. This is true for myself and my daughter who also has been increasingly congested, only at night, since it has been so hot out. I try to give her some relief by using saline nosedrops before she goes to bed and trying to make sure that she gets plenty of liquid.
Good luck!