At this point in medical history, with the number of people that didn't know they were participating in an ad-hoc longitudinal study over decades of how well or dangerous the accepted standard inoculation schedule is, I get the feeling you're couching close to conspiratorial thinking as "healthy skepticism".
The vaccines themselves and vaccine scheduling change over time. How would we know if something harmful was introduced?
Unless of course as you state we are unwittingly participating in ad-hoc longitudinal studies.
There are any number of `modern` diseases with seemingly unknown causes. It's not a stretch to be skeptical of the safety of modern medicine in general.