Cleaning the EGR valve should help lower NO, if in fact your Honda Civic is equipped with an EGR valve. Honda Civics equipped with 1.5 or 1.6 liter engines are typically not EGR valve equipped. If however you happen to have an EGR equipped Honda Civic do remove the valve and clean the intake and exhaust manifold passages as well as the EGR valve itself.
The cold air intake system should not have much affect on NOx since it should be installed before the mass air flow sensor and all air entering it should be metered. We would recommend ensuring all intake housing fittings are tight and air leak free. Unmetered air entering the combustion chamber will cause high NO.
As fas as the Catalytic Converter... typically when a non-EGR system equipped Honda Civic is diagnosed for a high NO fault the CAT is suspected of being defective. This should only be assumed however after all emission systems have been inspected, especially the air/fuel control system.
Nox is created when engine combustion chamber temperatures rise above 2500f. There are a few reasons your Honda Civic could create high NO. Two main things however are a lean fuel mixture, which is typical of a vacuum leak. A vacuum leak is basically unmeter air entering the intake manifold. The second is a defective EGR system (if your Honda is equipped with an EGR system).
The final emission component to be suspected of failure on your Honda Civic is the Catalytic Converter.
For more NO faults follow the Link below:
What Causes High NO?