I've been flying squares (and occasional triangles) for a couple of years now, as most of my latest birds have been four (or three) rotor helicopters or four airbrake models. While I am sure there is some additional drag from the "corners" as opposed to a round body tube, I've been really happy with the altitudes the have reached, and I have lost some rockets due to thermals.
Two great things for SCRATCH builders of square rockets.
First, the manufacturers will tell you that often the most expensive part of the rocket is the NOSE CONE. With squares or triangles, you don't have a nose cone, you have a nose PYRAMID. These are easily shaped out of cardstock and tape or glue, dirt cheap. They weigh almost nothing (which may be good or bad, depending on your CG/CP needs.)
Second, it is REALLY easy to put the fins on, cuz you can just lay them on the side and let them hang over the edge. The will look asymmetrical from the front (think pinwheel), but they work just fine. They do NOT cause any rotation of the rocket.
Probably the hardest thing is motor mounting, you have to cut two custom "centering squares" in place of the typical "centering rings" used on body tubes. Even this is not that hard. For about $6 delivered I got some 20 and 24 mm hole saws (you can also cut them by hand.)