The USGS NHD+ Users Guide includes a very detailed description of the technical process:
A collection of streams go uphill in this map where in reality I believe they flow into an underground pipe or something that drains into the lake in a different place. I wouldn't expect the underground section to be perfect, but the hill the streams ascend is ~50 feet.
In another place two ponds are not shown, maybe due to dense tree cover? I believe both have water year round, but one was fenced off after a kid drowned and the owners may have filled part of it in.
I believe that the NHD+ dataset uses an alternate strategy; it burns an artificial channel into a sink, connecting it to a lower-elevation outlet. The dataset includes attributes that identify these "underground flow" segments. I didn't examine ESRI's Living Atlas site closely enough to see if they've used a different symbology to represent these segments, but your comment makes it sound like they did not.
A pond often has no inlet and no outlet (as opposed to a lake), so it makes sense that some ponds may not show up in this dataset.
I checked the Lost River and some of the other areas on the Snake river plain. I can see how it would be hard to deal with water flowing underground. I noticed that the lava flows have effectively no streams, which I guess shouldn't be a surprise but it was.