If you watch a bit more MMA, you'll note that for instance, when GSP or Lesnar or Hughes do doubles in MMA, their knees don't touch the ground - you only have to do that if your opponent is crouched over as in various grappling competitions. So every one of GSP's opponents, and Lesnar's, and Matt Hughes, could have thrown knees to try to stop the shot. And yet GSP has something like 80% success rate with his shots, and his percentage is going up, not down. Doesn't that make you suspect that it might actually be a lot harder to do than it looks like from the safety of your couch?
Saying hit the guy with a knee when he comes in is prime "anti-grappling" Kung-fu youtube instructional stuff. It says a lot of your understanding that you seem to believe it really works that way. Try training a bit, and you'll understand why in practice its very hard to time an incoming knee onto a shot (and like I said, its perfectly legal for most MMA doubles, because they don't go down to their knee).
Not sure about countering knees to the head from North-South, I'll have to try that in the gym. I suspect its not as easy to counter as you think, but I'll have to play with it a bit to see.