It is indicative of a real and significant moisture problem.

This moisture affects your wood moisture content.

What caused issues, too much moisture under the house?

It gets insane heat and moisture too.Regarding zoning, I have another house here in Denver with a garage 1 foot from the property line that I just built last year.  

(I did have a friend who is a waterproofer look at it the time I witnessed the outside flood, and saw water inside, and he indicated installing a sump may not flow enough and also allow an easy spot for penetration)2.

I suspect moisture damage on the laminant in one room is from pee.

None of the problem areas are in exterior walls, so I don't think moisture is a factor.

I am taking down a few small trees on my property to get a little more sunlight on the decking and reduce the moisture, and I'm hoping the neighbor will remove the bigger one on their side before too long, since it's too close to their house and will have to go eventually.

Moisture in our environment is a real issue and although I haven't heard of this situation, your uncle's explanation makes sense to me.  

Be sure everyone entering and handling that mess wears some appropriate safety gear - breathing masks, at the very least, head covering, eye protection, good strong gloves resistant to penetration and disposable outer wear which is discarded at least daily, or as needed when heavy soils are encountered.Consider going hazmat compliant.