He knew that Clinton was lying scum before he even got elected. In fact, he sat at a round table interview with Bubba at the Rolling Stone Magazine offices (or at least the interview was conducted by and for RS).
Hunter S. Thompson just chose to hold his tongue. He's a drug addled old partisan fool. I read Hell's Angels and Fear & Loathing In Las Vegas. I haven't been able to tackle any of his later works. It appears that he is aware that the 1960s ended but he never accepted or got over it.
Been meaning to dig out that issue of RS...interview was at a greasy spoon called Doe's Eats, if memory serves...and it does. HST was pretty adamant that he was taken in by Clinton in the last blurb that I saw on the subject.
Try reading The Great Shark Hunt...a little less Gonzo than some of his stuff.