I am new to OpenGL.
Wondering if there is any good Scenegraph API/framework for OpenGL.
At the moment I am using glut with a custom node based solution: I am setting children and siblings for each node the calling a traverse function.
I'd like a more flexible solution when it comes to managing dynamic elements in the scene.
SDL is a bit more up to date than glut, but you are on the right track with rolling your own graph structure to manage scenery. There are plenty of frameworks available. OpenSceneGraph, for example, has been around for quite awhile now. OGRE has a large following as well. However, it is not a strictly OpenGL library as DirectX and software renderers are also available.
You may want to look into related topics like binary space partitioning, quadtrees/octrees and kd-trees.