I didn't do a boat dive until my 8th (last) trip to Bonaire; did Mi Dishi off Klein Bonaire (nice dive; not really superior to the better shore dives off Bonaire) & Small Wall (reminded me strongly of The Cliff, only bigger). It was okay, but I went back to shore diving.
Safety: I've read about stuff being stolen from vehicles, are there any other concerns?
Standard practice is leave nothing of value in your vehicle, leave the windows down & doors unlocked, and if petty thieves search your vehicle while you're diving, hopefully they'll move on and harm nothing. Take a small waterproof container for keys & spare cash. The rule of thumb is if you'll get bent out of shape if it's missing after your dive, don't leave it in the truck. Take your chances with cheap sunglasses, empty soda bottles repurposed for bringing drinking & rinse water, etc...
There are reports of other crime on Bonaire, yes, as there are probably anywhere you go with a population, but it seems to be regarded as a pretty safe place, in terms of personal safety. Walking outside after dark, that sort of thing.
You can rent an automatic transmission truck at extra cost if you arrange it well ahead of time. At the end of the week, a fresh tank of gas is going to rip you a new one, so be ready for sticker shock at the pump.
When you eat out, don't assume there are free refills on sodas. Get water at restaurants and guzzle your sodas at the room. If you like over-the-counter meds on hand, such as Ibuprofen, Benadryl, Bonine, Sedafed, Triple Antibiotic Ointment (e.g.: for scrapes), etc..., take it with you. Last time I was there, I didn't know of any 24 hour drug store type place,e and no Walmart. It gets pretty dead at night.
Richard.