The real question centers around the kind of engine that happens to power a specific scooter. As discussed many times on this website, older European scooters from the likes of Vespa and Lambretta used carburetted 2-stroke engines with nary an environmental standard to adhere to. Today, things are different. Nearly every scooter (including recent Vespas) sold in America at present is equipped with a clean-burning and fully modern 4-stroke engine with fuel injection.
Also, there is a difference between carbon dioxide emissions and other pollutants that is often overlooked. The amount of carbon dioxide spewing out of a vehicle's tailpipe is directly proportionate to how much fuel is being burned. So, a more fuel efficient vehicle will emit less CO2. Other factors like hydrocarbons, carbon monoxide and nitrogen oxides can vary widely and don't necessarily rise and fall with fuel efficiency.
As time goes on, motorcycles and scooters will need to meet the same emissions regulations as cars and trucks. Right now, not all scooters are created equally, but there are many more clean emitters being sold today that dirty, old-tech machines.