I know I'm not seeing quite as many as I was a couple of years ago, but I suspect it's a localized problem, driven in large part by plague. I can't say I've read many studies on this subject, but I'm not seeing as many around in my usual stomping grounds.
There was a news article the other day about a plague-infested colony near Boulder, CO. I also know that I haven't been seeing p-dogs around at the place where I typically shoot. It's a private land location, where there was once a shooting club. Back when the club was active (until about two or three years ago) the members often shot the members of this colony, which was conveniently located down the rifle range. Despite lots of shooting pressure that colony always thrived (admittedly the shots were usually 500-750 yards, so there weren't a ton of folks who were skilled/equipped enough to plink those dogs). Anyway, despite the area hardly seeing more than a couple of riflemen per week these days, I haven't seen much in the way of prairie dogs all summer. The grass is growing back where the colony was, though the holes are still there. I suspect plague killed many of them, because there's nothing else out there that would have likely wiped them out.