Prop guards definitely will have some effect in the wind, but I agree with the others; mounting dual batteries outboard of the fuselage not only has an effect on how efficiently the prop wash can clear the fuselage, it also dramatically changes the roll inertia (polar moment of inertia for those who are counting) by moving the most massive parts of the aircraft further away from the center of gravity. You're gaining battery capacity but adding weight and sacrificing maneuverability (maybe improving stability for video/photo use, though...)
For what it's worth, you can get virtually identical flight time (maybe better, since the aircraft doesn't have to work so hard to maintain attitude) with a 4000maH Multistar battery for $25 and it fits in the battery compartment with just a little trimming behind the battery door, so it minimized any effect on the flight dynamics.
That said, I'd really suggest you try ditching your double battery and prop guards and see if it flys more like you think it should... if there's something "off" in the NAZA tuning, you should probably figure that out.