Yeah, a 9" often does and can have different length axles side to side but depending if you want the pinion in the center of the tunnel or the pumpkin in the center of the tunnel (depending on if it's a custom or off the shelf) determines the length of the axles. If the pinion is (kinda) centered, with an offset pumpkin, as is the case of most aftermarket 9" housings, quick, TRZ, speedway, etc., the brackets are biased to one side of the housing more than the other. Just buy whatever housing you like, and wherever the pinion lines up is fine.
But like I said I assume you are talking wheel mount flange to frame relative to each side. You want the same gap between the wheel and the frame on the driers and passenger side. If the wheel mount flange is not centered relative to the frame, the tire will hit the frame on one side and not the other.
As far as using the upper control arms to center the housing, yeah, adjustable links are primarily to adjust pinion angle. If you make the bars slightly different lengths it can help put the housing where you want it left to right. Or lower arms too if they are adjustable.
If you are hard core drag racing and yanking the front wheels off the ground for 200ft, and worried about putting rear steer in the car so it launches straight yes, the upper bars should be the same length. Slight lengths in upper bars can make the car push right or left. Hard core chassis guys will have really long calipers to dial adjustable arm length in PERFECT because it can matter that much. That is for 9 second or faster stuff.
Personal experience, I have my upper control arms set up to be different length and an running bottom 11's with a stick shift car and don't give 2 craps about rear steer. I don't yank front wheels of the ground. I put my housing in the center of the chassis, and run 15x10's with 275 drag radials. It doesn't cause any problems. The arms might be 1/4" different in length.
No need to over think it, buy an off the shelf housing, buy your wheels. If the wheels clear the frame on one side and don't clear the other side, get some adjustable upper arms and set pinion angle and adjust the uppers relative to each other so both wheels clear the frame.
I can't find the thread but I remember there being a topic on the forum here where GM had purposely made different length hole-to-hole upper control arms for G bodies from the factory. I'd give someone a virtual high five if they can find that thread with the parts book. Even GM played with different length arms to get the housing centered if it was really bad.
