I think the second point is valid, to a certain extent, because IQ is only a partial measure of mental faculties of a person. In fact, it is highly probable that APTX 4869 shrinks people who have higher neural activity, and kills those who don't. Shinichi is a detective with exceptional skills of deduction and acute observation. Haibara is a scientist, hence her thinking capability is a bit higher. It was also mentioned that she was a prodigy and started working for the Black Organization at the age of 13. Hence, Shinichi and Haibara shrank. Others didn't, and died.