If he is wanting a bottle in the middle of the night, you need to decide if it's hunger or he's just thirsty............I would ask him if he is awake enough, if not, then try to give him some more food at supper or maybe change the bottle for a night type healthy snack..........dried fruit or something he can eat........
See if that helps.........it sounds to me that he is hungry......but who knows..........
If he drinks out of a sippy cup and you trust that, you could sit a sippy near him in his room so he can wake up, get a drink and go back to sleep...........just make sure he doesn't get too much water or juice to spill everywhere.
Good Luck and take care.