Why is the USB connector the shield connected directly to the GND in the Arduino Due, and through a resistor R1 and a capacitor C1 in the Arduino Nano33BLE (see schematics)?
Differences in design philosophy. The intent and action are for the most part the same.
I added two more circuits (see below): with a choke and without a connection at all. I see no system, no philosophy. Can you provide more details or links?
The design philosophy is to effectively connect the shield to ground, to block EMF radiation. There are several ways of doing that and they all work. You posted three of them.
Ask the engineers who designed the circuits why they chose one option over the other.
As an aside, the main difference between the top two circuits is that with the R/C option, large currents won't flow if you accidentally connect a voltage source to the shield.
To avoid such an accident, never change wiring when the circuit is powered up.
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