Yes, there are a ton of underground tunnels all through the county. Houses occasionally sink into them! I'm not so sure there are easy accessible enterances though. I think once abandoned they block them.
Trying to answer a few other questions:
The local ER is open all night every day in Boonville. I'm sure the police have looked into that.
Not much else stays open late in Boonville. The Walmart here says 24 hours but I swear I've gone there before 8 am and they've been closed, so not sure it's accurate online. I'm not sure about gas stations but I think the only things open that time of night are the bars.
The example picture of a stripper pit is a good one, but not all have steep edges. Some are just pond size that has no tall edges but are a hundred feet deep or more. There are quite a few smaller ones in woods and forests that have filled with rainwater.
I don't know why they closed Scales beach. It's full this weekend (camping) but they do close the beach sometimes when they don't have enough staff to lifeguard or due to weather. Its has rained all weekend and you can't go on the beach if it is storming. It does look like swimming closes there Aug 10th, which is when the kids went back to school. I guess it's due to lack of kids to staff the beach area and lifeguard and is nothing unusual.
There are a bunch of people with the last named Scales down here. She is probably related but not necessarily closely.
"Narrowing down leads" to me to means they are eliminating the far fetched stuff they have had called in. I don't think they have much at all, but I hope I'm wrong.