The dramatic increase in the size of ships in the last century has stretched what might be considered a hazard to navigation, but I think in general the presence of shallows near shore is a thing to be generally expected and reflected in bathymetry (and proper non-OSM charts) rather than something to treated as individual features. 

If it counts for anything most Bahamian near-shore areas would be more natural=shoal than reef and telling them apart on imagery can be very difficult. 

Most of them are already within subsea=areas that the really big ships would tend to avoid. 