In general, the wire tangle is an integral part of any signal-routing system, whether physical wires in hardware, a replication of those wires in software, or a less skeuomorphic box-and-pin model like Reaktor (which itself has a hardware-style layer with "cables" called Reaktor Blocks).
The one drawback I find to replicating hardware, as VCV Rack does, versus something originating in the digital realm, is that more complex modules bring over their hardware-based UI compromises.
An example of this is the Plaits module from Mutable Instruments, called "Macro Oscillator 2" in VCV Rack. The hardware Plaits module is very compact, and uses a series of LEDs with little icons next to them to denote which DSP algorithm it's running. The only way to know what anything does is to look up that icon in the manual and read what each of the knobs do in that mode.
In a software-first paradigm, the UI would use a software UI pattern rather than a hardware one, most likely a drop-down menu instead of a row of icons, and the labels on the knobs would change based on the mode (this is actually how a port I'm working on of Plaits to the Reason environment is designed).
All that said, many modules in VCV Rack are quite simple and would be no different if they originated in software. Things like basic oscillators, envelope generators, and filters need no manual diving if you understand the fundamentals.