If you see this in your dog, I hear you. It's very possible your dog's behavior looks suspicious, and that it means something. But it probably doesn't mean what you think it does. In 1977, Peter Vollmer, a veterinarian in Wisconsin, had a client who complained that his dog, Nicki, shredded paper in his absence. To investigate, Vollmer recommended that next time, the owner shred the paper himself before leaving the house. When the owner returned, the dog looked "guilty" even though she did nothing wrong.
Why did Nicki look guilty if she hadn't shredded the paper? "Evidence + Owner = Trouble" summarizes Frans de Waal, in the acclaimed book "Good Natured: The Origins of Right and Wrong in Humans and Other Animals." Meaning, dogs are responding to those things in the environment or situations which they have previously been scolded. They're fearful or upset, and our concept of guilt is not part of the equation.
Submissive behavior has an additional component in the social world of dogs. Dogs offer submission actively, without prompting, and often to members of their group who are not acting in a specifically confrontational way. So your dog might look guilty before you find that half-eaten shoe because what she knows is that when you see things chewed up, you get unhappy.