If you have an external DAC, yes. The headphone plug is outputting analog through the internal DAC and amplifier, so there wouldn't be any point to an external DAC. External components have the advantage of better components and isolation from the EM noise generated from high-speed switching.
I do not know if 3.0 is better or worse than 2.0 in terms of noise, but your DAC might not even be compatible. I don't think the Schiit Modi works with 3.0, for example. Although, 3.0 might be worse if you are operating at 2.0 speeds. Remember, the noise we're talking about is coming from high-speed digital switching, and USB 3.0 is faster than 2.0, so there might be some extra noise inserted. I would have to pull out an O-Scope to check this, though.