Personally I'm preferring non-clustered designs over clusters. In low rep levels the cluster works well because players are still learning their hacks and are easily caught out with their ice wall/protector timings. As you get further up in reputation naturally the competition is harder. By this time a good hacker is quick enough to 9/10 times replace their shields immediately or even use a shocker for that matter and disable everything since it's clustered.
Not only that the point of most choke-points (where else would one cluster..
)isn't to stop an attack but to slow them down, by using clusters I feel you give the hacker much more room to move since the can hit multiple nodes at once and shut you down faster.
Important thing to note,
1) We want our attackers to spend time and programs as much as possible, clusters can potentially do neither. Yes they can overtake a node and kill the programs there handily but more often then not what happens is they Ice wall and protector, the start hitting your other nodes and so on. This means once they open up one more node they have the ability to secure that and use one set of programs to take out all the rest.
Eg. You have a scanner connected to a black ice and two turrets, these all are wired to a guardian and scanner and turret, and in turn connected to each other. Hacker takes one node, from this node he/she can use a set of ice wall/protectors and offensive programs to hit each other node one at a time. Yes they may have to add another two or so Ice walls however you basically end up saving the hacker more programs this way. Alternatively if they use programs on each node they secure, the may waste some programs but they speed up the process and you save them time.
But hey it's all about what you feel is best!