The USB Jacks on the Raspberry Pi simply passes through the input power supply. I suspect a wiring fault would fry the RPI before it fries the controller . Instead , too high a voltage is my suspicion I would use a multimeter to confirm the USB voltage at the business end of your USB cable
. Short circuits between power lines would not likely affect the controller but damage the pi or it's power supply , short circuit between data and power may damage the logic on USB SNES controller but would likely also be associated with intermittent connections and other glitches. The fact that your controllers fail with such regularity after functioning fine indicate to me some fundamental power supply issue, but may still be associated with a short circuit , a multimeter would be useful there as well .
I would try a powered hub and replacing the power supply for the Raspberry Pi . I would also replace the cabling while I was at it .
Note that significant power AND ground voltage spikes may be present in a car environment , so isolated supplies are highly recommended . Never use chassis for return current/ground as it is extremely electrically noisy. Note that if the ground "jumps" or "falls" due to noise, the effective input voltage also jumps, even when using a regulator.
Internally the raspberry pi has a regulator for 3.3V that can handle a wider range of input voltages even up to 9V, however if your power supply is supplying too high a voltage it may still cause damage to downstream devices.
The USB spec is very narrow, the required tolerance is 4.4-5.25V so devices can be very picky about about input voltage and may not tolerate much more than 5V even if the RPI is ok, the input votlage clamp on the raspberry pi is at 9.2V so up to that voltage may be delivered to attached devices if there is a faulty or incorrect power supply delivering too high a voltage for the USB controller.
I would try a powered hub and replacing the power supply for the Raspberry Pi . I would also replace the cabling while I was at it .