Chad, you are right, white sucker can and do exist everywhere. Their mere presence does not mean the habitat is poor. Good numbers of them relative to trout and other sportfish definitely indicate problems, especially with sediment.
Here's why you may see so many in CPW surveys. Many, if not all, of even our best trout fisheries in Colorado have noticeable sediment problems. Sediment occurs due to mining, grazing, logging, and urban development. And it sticks around. Sediment from grazing alone tends to stick around for upwards of 50 years before the river is able to re-equilibrate. Sediment from mining will be there basically forever without some kind of major renovation. So long as sediment remains, sucker populations will thrive. Sediment changes the aquatic insect community to more burrowers and worms, which the suckers can sift from the sediment but the trout can't get to. Then there's whirling disease, which relies on the tubifex worm - a sediment-dwelling worm - to complete its lifecycle. So sediment is s double whammy for trout: depresses food and kills their offspring.
I've spent a few summers in Idaho and other western states. It's striking just how obvious the degradation is now that I've had the privilege to float and fish the Henry's Fork, South Fork, Gallatin, Flathead, Yellowstone, Salmon, etc. Each of these rivers are wholly or mostly wild trout water. No or very little stocking. Whirling disease is a concern but not a key threat. The habitat is just so good - and sediment-free - that whirling disease just doesn't have the same kind of effect. There are still suckers, of course (not white, mostly Utah). But there are way more trout.
That's the way I see it. I know, it's very anecdotal - I don't have any real sediment or insect numbers to show you to prove my point. I have only what I've experienced - and that's a lot of fine sediment in Colorado and not a whole lot of that kind of thing elsewhere.