Palpatine's hatred of non-humans seemed like more of a political tool than a deeply-held personal belief. All dictatorships require an obvious enemy for the opressed people to focus their misery upon, or else the dictator will eventually have a massive revolt on his hands. It was useful to get the masses stirred up with xenophobic hatred since it A. made them easily manipulated, B. distracted them from the real cause of their troubles, and C. all the resulting bad vibes kept the Dark Side strong. The Clone Wars seem designed to engender this sentiment: All of the agressor Seperatists are non-humans (except Dooku, of course), the mixed-species Jedi are overwhelmed by the conflict, and only an army of cloned Humans is capable of defending the Rebublic.
As for Palpatine hiding his Dark Side aura, I would imagine that Darth Bane or one of his early successors would have devised a technique for cloaking or negating their presence in the Force, much as Ysalamiri do, or the Sith could not have remained hidden for a thousand years.
