I haven't seen any mention of dive flags for the shore dives.

Here in South Florida even with a dive flag it can be dangerous, but am I right in presuming that in
Bonaire there isn't much boat traffic and you don't use flags?

Dive flags are used on Bonaire but some other differences factor into this. For example, our dive sites are marked on shore and permanent mooring bouys are at the dive site. It is required by law that all boats stay at least 50m (150 feet) away from any boat mooring unless of course they are tying up to it. So if you are diving a moored site, you already have the safety zone. Plus any boat can easily see a vehicle is parked on shore so they know somebody may be in the water. Plus the rule about only "dead slow" travel in the light blue water or shallow water areas helps too.

The one serious place we always use dive flags for is in the Kralendijk harbor area and the yacht moorings. Our monthly underwater cleanup dive uses 2-4 flags depending on the size of the area we are covering that day. The boat traffic can be heavy with lots of dinghies, fisherman, sunfish, you name it. Although the dead slow rule applies and all traffic should pass around into the deep water, it does not work well in the harbor.