Hello,
this is partly by design; hitting Delete will hide the nodes, but maintain the connection, hitting Shift+Delete will delete the nodes/materials (general changes to the document) - This is a limitation from C4D that we worked around in this way (hints to this are written in the right-click menu).
What piqued my interest is "This can then cause that the object with the material is not rendered". This is something that's been bothering us for some time now, can you reproduce this consistently? If so, could you shoot a short video for us and/or provide a scene with steps to reproduce this? It would help us immensely.
Thanks,
Jan