re: Why does my dog have this annoying habit of...

Leave a light on for the dog. A nightlight.

Perhaps you could put him in a crate or a pen in your bedroom.

Give him a bone to chew on when you go to bed.

Make sure he has a water bowl.

When was the last time you fed him? Do you only feed once in the morning? Perhaps you should feed him twice, once in the morning, once in the early evening.

there are a lot of reasons your dog is barking/whining; he's trying to tell you something.

Yes, they can be doing it many times for apparently no reason, but if you try enough things, I bet you'll figure out what will satisfy him.