You completely agree with me. You said:
See ? They were once considered (i.e. believed to be) supernatural, and it turned out they are not.
Nothing is supernatural, everything is natural. Whether we can or can't measure or understand something has no bearing on reality at all.
Supernatural means 'above or beyond nature'. And it just so happens that nature encompasses all that exists anywhere and anytime.
A definition of supernatural means 'above and beyond nature'. Another would be something that is undefined by natural law. A definition of 'natural law' is when nature is observed and recorded to act a certain way every time, everywhere. I.e. gravity, rainbows, lighting.
If there is no human observation and discovery of the way a natural event occurs, it is 'supernatural'. When man did not understand lighting, it was a supernatural thing. we now have a law for it, but truthfully when there is no law, it is supernatural and it was not incorrect for one to believe that.
In a philosophical sense, or to God, there is no supernatural. To man the pursuit of understanding the supernatural inspires him to investigate God and/or the mechanics of nature. If man maintained the idea throughout time that there is no supernatural, there may not have been an investigation in to science as much as there has been.
Investigating the supernatural either through science or spirituality leads to understanding.