We generally don't employ hypnosis. Sometimes we even skip the hypothesis step, because "what the hell is that" is enough to start generating data. Don't confuse all of scientific research with the scientific method; it's just one method of investigation.
A theory is usually based on some prior knowledge or observations. But let’s forget that for a second. In the anti-vax case, their argument is: “All your research in favor of vaccinating the population is wrong. We don’t have any evidence for it, but you should turn your public health policy 180 degrees!”. I don’t why it’s so hard to grasp the issue.