I'm not going to take my cleats off to confirm, but I'm 98% certain that my year-and-a-half old cleats are of the same design. I'm about 70% certain that the 2-3 year old cleats on my old shoes are also of the same design (I'm away from home currently and can't confirm). Regardless, I don't have an issue with countersunk nuts as fasteners given the application.
IOW, I don't think that the changes can be attributed to Wahoo and, even so, I don't know that wagging a finger at Wahoo and/or Speedplay is warranted; I think that the current cleats are *much* better than those of 5 or 6 years ago.