is he nicely warmed all over with his pajamas?
he could just be cold at night! i just made hubby get his own blanket. darn it i'm 42 and he kept pulling them off me and i was waking up 4 times a night. since he started using his own, i don't wake up AT ALL.
those feet pjs are the best. i wouldn't worry that there is something physically wrong with your son. i would assume:
1. he's cold
2. draft in room
p.s. it is better that he pees a lot than he doesn't do enough. that is part of how our body gets rid of toxins, so never try to do something to curb that. keep feeding him as you have been, don't compromise his growth/nutrition. i bet it's cold at night in his room and that's why it's happening. here in the desert temps drop very drastically, and since he's not doing it during the daytime...that is another sign.