I am not sure what you mean by the buffers are neutralized. Buffers occur as speciation of chemicals depending on the difference of their pKa value, and they are never neutralized. The acid you use to change the pH is the "buffer" problem most people observe. For instance, when people use citric acid, it has THREE speciations at close pH levels and will cause buffers whereas HCl or sulfuric acid will not. Of course, when you throw other chemicals in there from tap water, you can get other buffer effects you can't hope to calculate. Unionized distilled water is the best way to go, but most of us don't have the resources for that. RO water comes out ionized, typically. I'm not sure what anion/cation resins are, but I think you might mean the ionization of the water? Or is this a substance you have used in hydro before??

Yes, certain nutrients precipitate at higher pH values; hence, the reason they are not available, but research conducted by UF for commercial applications showed differences in relative yields were not statistically significant. The nutrients were 5-10 times lower at different pH (including 8), and even at 8 the yields were fine. AP systems are quite complex with microorganisms we have yet to realize. Experimentally observed results that seem to defy our common, hypothetical, and theoretical knowledge is what really helps us understand AP better!