Having lived on Bonaire I have to say that "news" articles are pretty low on details. I've had dinner with the owners of the BES a couple of times but they were so nice I didn't bring it up. I think it's just the Dutch style. I find the same thing in the news in Mexico though...
I had more than a few close calls with boats and boat related activity there for sure. Anywhere near the kite boarding sites, even in the light blue slow boat zones their chase boats don't slow down, nor are they easy to hear as you ascend. Everyone knows you're supposed to go slow inside the mooring buoys but not everyone does. STINAPA is not helpful on the topic when contacted. I know, I tried. My practice was to remain submerged until I could stand up just offshore.
Another incident that shouldn't have been legal but actually is: My wife and I were diving the Salt Pier. I saw an illegal anchor and went to investigate it. I took a photo and then a perfectly legal cement block anchor came down right near me. I signaled to leave the area because what was coming next was fishing lines with good sized hooks on them. I'd already seen a snapper with a brand new hook and a couple of feet of line a while before. I surfaced and got photos of the boat with the illegal anchor and then we moved towards shore. The boat went under the Salt Pier and they cast more lines right down among the pilings, and diver's bubbles. Completely unsafe and yet it's perfectly legal to fish at the island's most popular dive site.
We were lucky to figure these things out without being hit by a boat or snagged by a hook but I still can't figure out how an island that was put on the map by scuba divers doesn't take better care of scuba divers.