I can't see how cats wouldn't effect the readings. To my understanding cats utilize the O2 in order to work. That's part of why we have AIR pumps.

Now, on newer cars I have heard the cats are much more sophisticated. The new cars run a much leaner/efficient mixture, meaning there is not enough o2 in the exhaust gasses to make the new cats work properly (which is why if you just took a brand new cat off a brand new car and stuck in on your car, it probably wouldn't make you pass emissions through the sniffer) The new cats have a reaction that causes Oxygen to be created...or so I have heard.

All in all a perfect world would see us using a stand alone and doing individual cylinder tuning (fuel and spark) for the best possible power. You would treat each cylinder as if it were its own separate motor.