I guess technically it could...if the intake alters the MAF signal (which lots do), that can alter affect the fuel and timing maps the ecu runs, which can alter emissions

 

I don't think they can really negatively effect the emissions, unless they mess with sensors, or vacum lines in a bad way.
You can mess up some emissions with working on intakes, but almost always there is no problem.
also, it's just a matter of the company getting the certification for the intake being CARB legal, intakes that aren't cans still pass etc...