CNG light duty vehicles are subject to the same smog check rules as gasoline or propane. This is nothing new. I have had no trouble getting smog checks when due on a '00 cng crown vic and '01 gx. My '08 will not be due for a few years.
A cng vehicle can have problems causing excess emissions.
Test equipment at any CA smog check station can test your car. The tech may have to search a little in the test software for the correct setup.