Although I own quite a few Spyderco knives, my knowledge of all the variations within a model is extremely limited. Given that, I may be off base here, but the only VG10 Natives that I have seen are Native III's and the only S30V ones I've seen are Native I's. If you are comparing the same knife, in these two steels, then IMHO, the difference will be minimal to non-existant. On the other hand, if you own a Native III and are contemplating the purchase of a Native I, then there are other differences aside from the steel that may make purchasing it more or less attractive to you.
The Native III is thicker overall. It has a much thicker handle and a very slightly thinner blade than the Native I. If you like the feel of the III, then the I may feel a bit too slim. If the III feels a tad thick, either in you hand or in your pocket, then you might prefer the I. Also the Native III handle is contoured, thicker in the middle, slimmer towards the butt end, with thumb and finger pads while the Native I is flat. The III also has a stronger lock spring, so it does take a bit more thumb pressure to open, but both are very smooth. The rest of the differences are almost pure esthetics, wire clip vs solid clip, raised thumb bumps on the blade vs thumb grooves, and the way the spine is tapered.