From what I understand I can have automatic MSAA for deferred shading in OpenGL 3.3 by specifying multisample textures/renderbuffers when creating my framebuffer (at a high memory cost). Does this multisampling also have any implications on the shaders, for either the geometry pass or the shading pass or is it all handled "under the hood"?
OpenGL 3.3 MSAA deferred shading
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Nope, you cannot have automatic MSAA in this case. It was literally called explicit multisample when it was first introduced to OpenGL for a reason.
You have to fetch each of the samples from your multisample texture and do the MSAA resolve yourself in the shader. Multisample color textures are a DX10 hardware feature, multisample depth textures are a DX10.1 feature but OpenGL makes this pretty transparent. Since multisample textures were not introduced to GL until after DX10.1, in most cases you get both (multisample color + depth) in GL.
I have an old answer here that might help to further clear things up.