Get all objects which are not visible to camera but are present in scene? These objects are hidden/overlapped by larger objects.
Or
Is there way to identify objects completely visible to camera from the scene?
This is a tricky task.
You could use some sort of occlusion culling to filter out all objects which are visible to the camera so only those are actually rendered. The related algorithms are not trivial and there is no official implementation for this.
There is also a WebGL 2 feature called occlusion queries that could be used in this context however it is not yet supported by three.js.