Sorry you had such a bummer of a trip. I have never stayed at Buddy's, but I did not like their reef, what with signs pounded into it and all. In fact it is the only site on Bonaire I have been to that I feel no need to return to. The beer at the bar there I found really expensive, and the food at Lion's Den was slightly pricey, but also very good.
As for the rest, I read in this thread the room broken into was left unlocked? Well, I guess. I never leave anything unlocked where ever I go. Maybe cuz I am a Jersey guy...
Diving in Bonaire is the best I have seen, save one site I found else where. Maybe you had a bad week? Went to all the bad sites? I know there has been some damage, and some of the big name sites were pretty thrashed after Omar, but still reports are coming in that much of the reef structure is fine. I am going next week so I will check that out myself...
The key to diving Bonaire is to go slow and really look around. Much of what is there is small, so if you are looking for big animals that is not the place to go. However if you want to see an ecosystem at work, full of symbiotic relationships, I don't think you can beat Bonaire for price and what you will see.
As for the leg breaker shore diving, most all sites have an easy access point, you just have to look for it...