There's no question that Thompson did a lot of speed in his younger days - he claimed that it made him prematurely bald. But, I don't think that anybody smoked it in the time period that Fear & Loathing took place in. Some of the strongest amphetamine pills were called Black Beauties, and you could get them by prescription, or from dealers. Shooting or snorting methamphetamine was also common, and more dangerous than the pills. I have a feeling that Hunter stuck with pills.

Has oil was also around at that time, and glass pipes were used to smoke it. That could be the answer but as someone said, it was probably just hash.