It is my understanding one shouldn't take color copy of naturalization certificate. It is illegal and can cause trouble if seen by someone. It was told to me by a Notary public. In fact Naturalization certificate clearly state in front that any type of photocopy is not law ful.
-Swadesh
Swadesh: It is INTENT that matters. If you make copies with intent to defraud, then even b/w copying is illegal. If you are making copies just for backup and for your own record-keeping, then it is not illegal. In fact, USCIS asks for a copy in case your original is lost or damaged!
I myself have scanned/stored electronically & made one good color and one good b/w copy for safekeeping. Ditto for my driver's license, passport, green card, etc.
But if you feel uncomfortable making a color copy for your record backup purposes, then don't do it. But definitely make a b/w copy before you send it off for your passport application.