Can a scene graph be stored in the GPU?
Short answer: Yes, It can be done. But no one does so.

Long answer: 
Scene graphs can be stored and processed on a GPU using OpenCL/WebCL. But it is not practical to do so. Updating scene graphs (a tree not in flat memory) on a GPU is slow, and processing it on a GPU is also slow (again, the tree is not in flat memory), while computing transformation matrices is cheap on a CPU. Thus no one is doing this.