Something has happened that has made him start doing this, it may be something you are totally unaware of, a loud bang that scared him one night or someone shouting in the street. It can be a very simple thing urinating and defecating give relief, make the dog feel better.
Firstly I would look at his diet, the fact that he goes to the toilet last thing in the evening, then needs to go again during the night, points to too much waste product in his diet.
Then I would look at his behaviour in general, is he confident or a worrier ?
He may be worried about being left on his own, as the previous poster stated.
Or he may be afraid of the dark, I know it sounds silly, but I have met dogs who are.
You may need to get him checked at the vets, to make sure there are no medical issues causing it.