vtkSmartPointer and vtkNew in VTK's API. Best practices?

Yes, writing code that is compatible with different VTK versions is just as easy to do in Python as in C++. For example:

if vtk.VTK_MAJOR_VERSION <= 5:
  threshold.SetInput(allSegmentsLabelmapNode.GetImageData())
else:
  threshold.SetInputData(allSegmentsLabelmapNode.GetImageData())