As far as I know, the overwhelming majority of USB headphones would have the same kind of DAC inside the headphones as the DAC inside your computer (unless we are talking about some audiophile headphones or something). USB can give you benefits like controlling the system volume level via USB HID controls. If the DAC is inside the headphones (instead of the USB end of the cord), the analog wires inside the headphones would be kept to a minimum distance and be somewhat less vulnerable to interference. If you have system volume controls on the headset and or software controlled button functions, you can bet the audio DAC is inside the headphones (not in the USB end of the cord).I think that specifically for audio 3.5 is better.
There are some good high-end 3.5 cables with noise reduction around there, as they have audio in mind.
While through USB you use a digital data cable, it's not designed to 'sound' better or anything, just to transfer data as best as possible.