well, there are no 'points' in Pride's scoring system. But yes, I do beleive they are instructed to count the yellow card against the fighter who received it. I beleive it counts as "1 successful attack" (for the opponent) or something like that.
Between the yellow and the weight difference, I was mildly surprised they did give it to Hunt. But the right decision was made.
About the only thing I can come up with is that they issue the yellow card for stalling/lack of agressivness, or in some rare cases when a fighter gets out of line with the ref (like the gracie fight tonight).
They take 10% off your purse AFAIK.
And since one of the Pride scoring criteria is agressivness, getting a yellow card should count against it.