That's true, 20 years wouldn't necessarily bring to light a delayed effect.
However the GMO case is interesting because we have in effect a massive scale natural experiment, where hundreds of millions of people on one continent have eaten lots of GMO food while hundreds of millions on another continent have eaten very little, over a period of 10-15 years. There is also a highly motivated group of people who bring to the public attention even the smallest evidence of harm from GMOs.
While I don't rule out a harmful long-term effect, GMOs are a long way down on my list of things to worry about, and dropping further over time.
However the GMO case is interesting because we have in effect a massive scale natural experiment
Not really, because the two groups differs in many attributes. You can't draw any reliable conclusions from that if you don't know individual consumption. If you could draw that conclusion we could conclude from US bee deaths that GMO's are bad.
But there also no reason to assume that risk from GMO would be equally distributed among different GMO foods. Letting plants produce poisons so that they won't get eaten by insects is likely more risky than doing some...
Basically: How does one pursue the truth when direct engagement with evidence is infeasible?
I came to this question while discussing GMO labeling. In this case I am obviously not in a position to experiment for myself, but furthermore: I do not have the time to build up the bank of background understanding to engage vigorously with the study results themselves. I can look at them with a decent secondary education's understanding of experimental method, genetics, and biology, but that is the extent of it.
In this situation I usually find myself reduced to weighing the proclamations of authorities: