From what I remember the sw they were working on in the novel was more like a Virtual Reality lego. I.e. something like what they use in Second Life, or possibly Minecraft, but I don't remember it being aimed at modelling sw architecture.
Also, by using a 3D sw you would lose the physical manipulation part, which seems to be important, according to the article linked above.
I have a feeling that legos are too "low-res" for sketching out software design. However, I use them sometimes before attempting a more detailed 3D model or illustration, to build a sort of sketch reference. I use this most when thinking about perspective, sight-lines, etc. It helps me avoid getting stuck in the minutia of my digital tools (Sketchup or Illustrator), where I can get distracted trying to make the tool do what I want.
I have definitely read about a project where they made a physical model to represent/show the complexity of a software system to their clients. IIRC the project involved doing a re-write of an existing system.
Unfortunately, I can't remember exactly where I read this. Perhaps someone else here knows the details?
Sorry I can't be more specific.
Has anyone tried lego or some other 3D construction set? Did it work? Is there anything particularly suitable to build "architecture"?