Paul,
You are absolutely right--the drainage may be perfect for those bunkers and I may have been too hydrophobic given that Atlanta has seen nearly 20 inches of rain since September 1st and I still shell shocked from the damage.
We were fortunate and have excellent bunkers ourselves constructed using the "Billy Fuller" bunker method and despite the massive flooding we had only one bunker that suffered any real damage and most required very little extra attention.
So, they may drain very well. But, they do look as if they form saucers and collect water from multiple directions and based on the one pic, it looks like they could form bird baths given a heavy rain.
The topic asked what's "wrong" with the bunkers so I was looking for something to be "wrong" and that was my first thought. I couldn't really see enough of the hole or know its par, length, width etc. to really decide if I thought they were "properly" positioned. Again, though, you are right that they could drain just fine.