Seems like some people are trying to run before they can walk and perhaps need to look at how clusters actually work in 'the real world'.
Never, ever would nodes be connected via USB. There's a special interface for connecting computers together, it's called a network interface and uses RJ45 cables. Just use a network switch to connect the nodes together.
As pointed out already, no need for KVM switches. You just log into a node via telnet, ssh, etc.
Storage. Well that depends on what you're trying to do. At minimum you'll need an SD card in each node so you can boot it and bring the node up. If you're wanting to build a cluster it kinda suggests that you want to use the computational power of several units working together to perform a computationally complex task. In which case you have one master unit which controls several slaves/nodes. The master unit sends out tasks to the nodes. The nodes processes the data then send the results back to the master. etc, etc.
In which case, unless you're working on very large payloads, only one large storage device would be needed connected to the master unit.
No HDMI option. Why? The HDMI connectivity is part of the CPU, it's not being made available via an external chip. Therefore, the only part you could remove would be the connector, which on a unit costing $25 would represent pence. In fact, due to economies of scale, it would probably save nothing when it came to the final sale price as you'd have to have different production specifications which would make the boards more expensive to build. Simply don't use it.