A few reasons come to mind.
On a great site with good contours and interesting features, you might want to use bunker clusters because that's what fits the land the best.
For example, lets say you want to put a diagonal carry bunker on the inside of a dogleg. The bunker needs to be quite big and/or long to acheive the desired effect. If you have micro-ondulations in that area that would host two, three, four bunkers or more to acheive the strategy, why destroy these micro-ondulations to build one large bunker?
On a bad site where you have to create everything from scratch, bunkers clusters can be used to diversify the look of the bunkering over the course of the round. In this perticular situation, I would personally use large bunkers on some holes, and small ones on others, while also mixing the two kinds (as well as their sizes) on different occasions for diversity. Of course, I would also try to create ondulations and movement that would allow me to do this in a natural manner....
So, in a word, it all depends on the land, and what you are trying to acheive, IMHO.
YP