Cover as far as what? An emissions test? Yes, and no.
For OBDII cars they don't use a sniffer at all. All they do is plug a basic scantool into the OBDII data link port and check for readiness parameters and emissions related codes. If the car is throwing a code, you fail the test. Technically you could have no cat on the car and pass as long as it isn't throwing a code.
Now putting a header on will always make your car throw a code because of the downstream O2 sensor. You can either get a tune to disable this sensor, or use an O2 cheater to pass.