The Properties Panel in a scene file has no tab for mesh when an object is linked to the scene. Can the Shape Keys influenced by a driver or is there some other trick to enable shape keys in the scene file?
To my best knowledge, your first assesment on having the shape keys be driven by bones or other control objects is correct. That is to say, shape keys can be controlled with drivers.
Often with corrective shape keys you've a setup where the shapes are driven "behind the scene" by the bone transforms. In case you require manual control over the shape keys, you can create a proxy for the controlling object in the scene you linked to.