My Theory on the Holes:

When the school was built, it was before public schools were required to have physical education for girls. So they didn't have a girls locker room or shower. But they did have a women's restroom there. On the wall where the holes are they had sinks, and the holes were for the water pipes.

When girls P.E. became required, the school had to expand the bathroom into a locker room and shower. The area where the sinks were was converted into the shower area. They took the sinks out, but the holes in the wall were still there, along with the pipes, but they could be unscrewed now since no water flowed thru them anymore. They also had the crawl space there incase there was a plumbing issue (and yes for the sake of the movie it was a huge crawl space.

How the boys found out about is still a mystery. Did the builder know someone who went there and told them about it. And the secret got passed down from class to class. Or was this group the first to know about it, and someone just kind of stumbled into it.