Night pains could be growing pains, or it could be the popliteal cyst or lymph node compressing a nerve. Usually, with an enlarged popliteal lymph node / cyst and neck ( cervical ) lymph node , I'll go for complete blood work and monospot test ( to detect mononucleosis/ Epstein Barr Virus ). Chronic bacterial and viral infection can lead to the enlargement of lymph nodes in kids ( also called lymphadenopathy ). It also happens in upper respiratory infection ( and if your pedi wants to explore further , I think they should go for a chest X-ray). Another thing that I'll always do will be the abdominal palpation to rule out enlarged spleen. In your kid's case , I'm still leaning towards the infection because he's otherwise healthy.
I have really appreciated your responses so far! Do you have any thoughts about the knee swelling/cyst and night pains?