Black Holes Appearing in Oak Floor
The tiny black specks that are not knots in your pictures are most likely from small particles of steel or iron causing staining. I wonder if your refinish process used steel wool (not a good idea on oak unless you are trying to stain it black.) The larger features with actual holes are, of course, knots, so if you have "holes that are not knots" you have not shown any pictures of them.

That new picture is a bit hard to see detail in (as you know) but there's certainly something knot-loke going on on the grain around it, so it probably is as well. Sometimes on an older floor that's been sanded down a lot you start to see stains from the steel nails, but that seems less than likely here.

To skip right to your water concern - probably not, since there's no sign of the floor buckling or failing to lay flat - wet hardwood floors tend to look like #expletive omitted# in short order as the bottom swells and the boards cup.