Equiloud (Uwe Schweer-Lambers) shares a quick tip that will allow you to use deformers with cloned objects in Cinema 4D. If you group your cloner under a null object, and apply the deformer on top of that, you will find that the deformer will distort not only the group, but the shape of the objects as well.
Using Deformers with Cloners could be annoying. But there is a work around with the Matrix Object!
This might not be what you are looking for, when you think about deforming a cloner group. If you want the deformer to deform the group itself, without the underlying geometry, you can do this be way of a Matrix Object. If you use the Matrix Object for the cloner, you can apply the deformer to that,and have the results you are looking for.