off-road pipe and computer

[Dino]

I was talking to a mechanic at the muffler shop and he said if I switched to either an H or X-pipe on my 96 GT, that it would cause the computer in the car to get all messed up (Check Engine light would come on), and that the car would end up making less power. Is this true? I thought I heard somewhere else about the Check Engine light coming on after the install, is there a fix for this?