2 things, IMO
1) glycogen holds like 3x its weight in water and on a low-carb diet you have very little glycogen and less fluid retention
2) if there isn't an urgent need to go that's waking you, it might be a mild form of insomnia. As your blood sugar goes down, your cortisol comes up. you might try a snack before bed and see if that helps.
If you feel well-rested, then I wouldn't worry about it too much. Sounds like you're doing great!