I haven't had trouble with nausea related to my pouch and I've had it about 20 years now. I agree with some of the other comments that it could be hunger. I had trouble with what you describe as a child and tween. I think it was low blood sugar and I grew out of it. I tend to eat a high protein high fat snack or dinner so I don't get hungry in the night OR have to go to the bathroom. Snacking before bed is tricky because of the pouch volume issue. Does the nausea go away anytime you eat something? Crackers might work better if thats the case because they will help with reflux better than candy.
Another thing could be having too full of a pouch. Is it related to anything you eat or how much gas you have? I can wake up feeling bad if I ignore my body and sleep instead of going to the bathroom when I should. I usually feel better almost immediately after going to the bathroom.