I think those examples are a bit misleading in that nobody actually prints 100,000 lines of code and looks at them all at once. So those examples are showing probably the whole "program" at once, which is impressive and looks daunting, same as a big textual code base.
Rather, in order to understand a certain aspect of the system, I imagine picking just one of the nodes and then asking the IDE to show me, say, the immediate inputs. Some of these may be semi-hidden (code folding!), others may show more detail, etc.
BTW, I've been thinking it would be great if these systems had a textual representation in the vein of Graphviz' dot language. So one could have the best of both worlds. For diffing, a simple textual diff could do, but one could come up fancier semantic diffs in the same vein semantic diffs for code or XML exist.
When I used Max/MSP a few years ago, a lot of people's code snippets looked like this, however, an important thing to remember is that the target audience for most visual programming tools are not trained software engineers -- ie they don't know about encapsulation and abstraction and all of the other concepts we take for granted.
I found Max/MSP code could look extremely tidy, as I would group my functionality together in a similar way as I would in a textual language (short single-purpose functions and such). You can write horrible spaghetti code messes in textual languages too, its just we've used enough textual languages to have learned how to abstract our code and how to organise it for maintainability. Its not an inherent feature.
