Nope, it eliminates the intake as being the restriction in the system. The motor will only pull in the air it needs but if the A/C is to small it will restrict what can be pulled in!
Your engine won't draw in any more air than it can use, the only thing that can accomplish that is a supercharger. The only problem would be if you've already had it tuned with a restrictive AC.
The more the merrier. That's why superchargers are so effective,they force air into the intake the engine would otherwise be unable to ingest on its own. End result is more performance. Engines run on air.