Pat,
On the courses I've mentioned there are probably anywhere from 4-9 holes with super contours, and the rest would not be considered flat. I would say super contoured requires significant features whatever shape they might take (tiering, shelving, mounding, rolls, dips, drop offs, areas of slope). I would think you'd at least need two of these features (a two-tiered green with no other feature would not count), and many include more. For example, I would consider #4 and 16 at ND super contoured. Off the top of my head, no other green on that course would fit the definition. #5, 10, 11, and 15 have interesting features, but would not be super contoured.
At Black Mesa I bet half the holes would qualify, with the stretch of 14-16 being the pinnacle.
Lost Dunes just about every green has significant contours of some kind or another. Its probably the poster child of an example. #4 is the champ there.
The Kingsley Club again has no greens that spring to mind of being flat, but all have interesting features again. #9 and #13 probably are the most dramatic.
I have no clue what the percentage would be, I doubt I've even seen 1% of courses built in the last ten years. The courses we are discussing are considered the top of the heap for quality as well. My reason for challenging you on this is that you said "no one" when these three courses, plus Friars Head and also Arcadia Bluffs would make a good start of five courses by five different designers that all have significant contours. I'd also add some of Jim Engh's work in that mix. While Pete Dye's courses may not always have "super contoured" greens, I don't think you'll find challenge lacking in putts from 30-60 feet which I think was part of your original point.