Why would the chip-makers bother? There is absolutely no incentive for them to do this.
They should do it because a tiny percentage of people known as flashaholics have a small percentage that likes flood to throw lights, and they dislike the square shape?
A round emitter would make no difference whatsoever, other than the shape in a fully throw aspheric.
The die is the most expensive part, made of semiconductor material (I think). They probably print a whole bunch of dies on one wafer. So you don't want to throw away the material to trim it down until it is a circle and lose output while you're at it. The only time you see the square emitter is with flood to throw lights all the way to throw or with a lens. For a regular light you can't tell the die is square.
Round would perform no better and would be more costly to produce something even remotely close in performance. Heck, square emitters are what make owning a high performance LED so much cooler than a regular old incan or cheap-ass chinese round emitter. Like dthrckt said, "it's hip to be square"!
Look on the bright side...shining that square beam on a remote building will light up its walls from corner to corner instead of just the center.