Nope, there's nothing adverse that happens. The car will be a bit of a bugger when it's cold out until it warms up though. You have to set the idle via the throttle body, it takes a bit of tweaking to get it right.
If you don't mind the clutter, keeping the stock idle equipment will make your life easier. I like the clean look and can deal with the funky cold starts.
The z31's ecu is anything but modern, lol.