Does the Geometry Shader affects the buffer of vertices and indices (VBO and EBO data in GPU memory) initially specified in the cpu side?
For example, suppose I have a vertex buffer containing three vertices, each with some attributes attached to it. Suppose then these three vertices are given to the geometry shader as input and the geometry shader outputs out a large set of vertices based of off the first three where it started with, generating thus a new polygon made up of more than 3 vertices. Does this process alters the content of the element array and vertex buffers?
Only thing I know is that of course it doesn't get altered. Because otherwise the next rendering call would generate even more vertices and that would be a mess. So where does OpenGL store the new generated vertices?
Suppose then these three vertices are given to the geometry shader as input
That doesn't happen. The GS is fed by the vertex shader's outputs. GSs never have any direct contact with the initial vertex data.
So where does OpenGL store the new generated vertices?
Wherever the implementation needs to. The rasterizer hardware will generally have a small buffer for primitive data to be rasterized. That's where the GS outputs will go.
But that's an implementation detail which is not exposed to OpenGL.