They are simply two slightly different approaches. The biggest difference is that the 'zone' system has a category for stuff that is ALWAYS in a hazardous exposure ... such as inside a gas tank. Many things rated "Class 1 Division 1" are not intended to ALWAYS be in such an atmosphere.
The other aspect relates to enclosure ratings. Many items - controls in particular - are of European make, and are specified in terms of "zone," rather than area. As with other enclosure ratings, the European classifications are not quite exactly comparable to NEMA designations.
Hazardous location practices are something that you really have to evaluate for each job, considering the specifics of each situation, and keep in mind the 'big picture.' There are several approaches that can be taken ... not all of them electrical ... and it's not always smart to mix approaches.
I suppose it's not so much a matter of using either the 'zone' or 'area' method. I think you pretty much have to use both.