In this TED Talk, a cyberwarfare specialist explains how using visual representation (and especially 3D visual representation) of binary data helps him figure out much faster how a device works, and how to attack it.

Makes me smile when I remember all the people who kept saying that the VR matrix was just cinematographic and had no realistic reason to be.

Of course there's a reason.
The IN UNIVERSE REASON is actually a very reasonable reason to use as the reason for stuff being the way it is.
Because the mind is not made to think in code. It's made to act on optical, tactical and audio input. Smell to a lesser degree for humans.

Somehow I tend to doubt that it involved making it look like alice in wonderland and then taking an infinite number of actions to find out whether a given blade of grass is really a web server.

Sculptured systems are a 3rd Edition invention that, then, was carried on. The idea is to make it difficult to identify stuff for the uninitiated, who have to scan each blade of grass to find out whether it's really a web setrver. Security through obscurity, in a way.

Imagine an arch religious hacker stumbling into a system where everything looks like gay porn.
Hope you have your reality filter up and running!

But aside from the specifically sculpted systems, anything else used SMTP(Standard Matrix Topography Protocoll) or something like that.
So outside of these systems, every node looked like every other node and so on.

Which produces the hall of mirrors defense in SR.

As this is supposed to be a help and not a trap I suspect they don't do that.

I've done a really minor bit of security visualization and it really don't have anything to do with the SR matrix concepts at all.

Yes, well, the hall of mirrors was not such a problem in SR3, because you did not constitute of a whole network of shit that does not work without knowing what the weather is like on the next continent.
the nodes look like a white cuboid standing on one tip but each node has it's own adress. it's just so you know "aha, this is a node" and then you check wether or not it is the node you are looking for or not.
In SR3, only big networks have more than one icon in them. A Decker/Otaku is just one Icon/His Persona.