Debatable. Some say its perfectly fine, some say its a horrible idea and not to do it. Personally I prefer the cars theft deterrent to work the way it was suppose to. Ive had a friend with a camaro (same style vats system) and his acted up so he did the bypass, which worked for a little while but then it messed up and they had to replace everything to get it back on the road.
Its a gamble and it really depends on whats wrong with the car as to why its doing this. If its that the key you have is old and you don't want to spend the money to get a new one, I say suck it up and buy the right key vs chancing something really getting messed up. If you don't know whats wrong with it, you need to start testing things vs just disabling the whole system, that causes problems down the road.