If you are just looking at global behaviour and not concerned about local values or max/min values this approach should be enough.
Ideally, if you reduce the size of the elements towards zero, your model will tend to a continuous gradient of structural properties. Yet if you stick to isotropic materials, your can discretize your material property variation : you can split the shell in smaller patches (or “elements”) to which you assign different properties. As far as I can tell Karamba3D does not yet support orthotropic materials (or any kind of anisotropy), nor does it support parametric materials.