I have used both square and round ducting in my experiments with centrifugal blowers and from my experience, with such short runs, they are a "Horse Apiece". The square duct is nice because you can fit it easily to a square fan base. My gut feeling is that with axial fans, round should be a little better aerodynamically, since the air that comes out of an axial fan is spiralling.
Rocknindy, your wording confused me as to whether the ducted blowhole will be blowing air into the case or drawing it out. In my opinion, blowing in would be a better approach if the HS fan is blowing into the HS. If it is exhausting air from the HS, then the blowhole should be blowing out.
There's no problem I can think of resulting from too much air blowing in, but the converse is not the same. If you put a powerful 120mm fan sucking air out of the case, it may exceed the airflow rate of the other fans that blow into the case. In that scenario, you would have a negative case pressure and be inviting dust to invade you case through every crack and crevice.
That's the Hoot Scoop