Comments from the wife, who has an extreme amount of knowledge in this field, as work and her Masters was on road side surveys and the validity.
The roadside counts have some validity- otherwise they wouldn't do them. Are they 100% accurate? No. But they give the agencies something to look at year after year to see general long term population trends. It wasn't clear in the article if they repeated the surveys. It doesn't seem like they did. Statistically, the fewer repetitions of a survey, the less accurate the results are. The additional surveys they conducted later in the year may have resulted in lower counts for a variety of reasons, the biggest I see is that the crops and grasses are taller, making it harder to see pheasants along the road. I think they even stated in there that the survey conditions were not ideal.
The spring hatch probably wasn't great- it was cold, wet, and long... It sounds like some hens nested again, but many times these broods are smaller. There is less habitat out there, which doesn't help either as far as overwintering.
I think that, yes, there probably are fewer pheasants this year than in previous years. I don't think that it's going to ruin the SD hunting economy though, and I don't think it means that you're not going to see birds when you're out there. Case in point- we've seen birds; just not roosters. I think lots of people will still limit out. It will just take them until sunset to do so, rather than noon (5 hours less of drinking... how will they survive?!). Hunters may have to work harder for the birds. Get over it. If someone is that worried about the state of the pheasants, then do what you can to create habitat out there for them. That's the biggest issue. The populations will drop if they lose habitat. There's no question about that. In the habitat there is, the birds are going to get a lot of pressure. So they probably will be more skittish and flush really early. But, since you can't shoot hens, the hunting pressure isn't going to change next year's hatch. Hunters aren't going to shoot all of the roosters in an area, there will be plenty out there to breed next spring.
In general, spend less time complaining online about how that hunting isn't as easy as it was 10 years ago and focus on doing something to change it (if it is truly that big of an issue for you).