there is no difference with the shape
Your biggest differences in ports is on how smooth is it, how straight it is, and whether or not it is flared. You toss in a 90 degree turn on a circle or square results will be almost identical. If you can use flares (square or circle) and streamline the port (keep it straight) you'll get the most efficiency out of it.
But even if you can do all that, if you make it too small your efforts of making it smooth are worthless.