Seriously, vanilla, I think you can discuss this with him in terms of scientific method, which he should be studying in school about now anyway. You can talk about how scientists come up with their ideas, that it’s dependent on proving something IS rather than proving it ISN’T.
And by all means, raise a skeptic. Could Bigfoot exist? Sure, it COULD. But given the evidence we have at hand and the improbability that such a creature could remain so well hidden for so long casts some doubts on its existence. However, it’s totally possible that tomorrow one could walk out of the woods, get captured, and we’d have to deal with it.
James Randi’s book, “Flim-Flam!” is a great introduction to skepticism and the paranormal. Read it and with him and discuss it with him. I know that I for one got grabbed by the stories of Randi debunking things and found that ultimately much cooler than the malarkey itself.
And please assure him that this isn’t taking the ‘magic’ out of life or ruining anything. You’re strengthening his brain, giving him good tools he’ll be able to use forever.
Now the problem, as I see it vanilla, is that, if I’m not mistaken, you have a pretty strong Christian background, and it’s possible that sooner or later your son will turn that tool on his religion. That may be a problem unless you know how to reconcile these things. I’m not intending this as an anti-religion slam, please understand, just a caution that this could cause a conflict for him unless you know of how to address it. I don’t know the details of your particular belief system, so I’m not sure how much of a problem that would be.
Good luck. We need more people being smart!