Plants take up nitrogen primarily as ammonium and nitrate. Yes clay particles are negatively charged, ammonium is positively charged and nitrate is negative. That's why ammonium nitrogen doesn't leach like nitrate does. Ammonium should be present even in clay soil as part of the nitrogen cycle and then converts ultimately to nitrate, but nitrogen is the nutrient most likely to be deficient because it doesn't originate with mineral soil particles. However, a nitrate test will only tell you the amount of nitrate and not the amount of organic nitrogen or ammonium that has not yet been converted so you might expect there to be more nitrogen in the soil than a nitrate test would show. Hope this makes some sense!