I just thought of something else. DD woke up this morning and came into our bed and we realised she had no nappy on. She said she wee'd in the night so she took it off. Then she obviously went back to sleep.
Maybe something like that? Totally random and probably not it, but worth a try maybe checking if he's wet and changing him? Maybe he doesn't like it at night how he doesn't get a new nappy when he wets? (No idea if you already do this or not but we don't change nappies until the morning if they're just wet).