Shouldn't be any negative effect. When I lived in Maricopa County I ran a bike that had aftermarket exhaust and Uni pod filters. The smog test was a static test, not a rolling road like the cars--WAY too much liability to put a m/c through that.
Only test done was at idle. In Maricopa County you're allowed up to 5.5%CO and 2,500ppm HC on a 4-stroke (2-strokes have their own standards), iirc. A jet kitted bike that's a skosh on the rich side will still only run 2.5%CO.
Reasons that bikes fail emissions are improper jetting, carbs that need a rebuild or, in the case of multis, out of sync carbs.
Last time I got the connie smogged she was running about 4%CO and 2,000ppm HC. Also was only getting 30mpg. Bike ran horrible and still passed emissions.