Well...I suppose in terms of the "letter of the law," sure it will affect your emissions legality.
The purpose of the "Nutter Bypass" is to put the emissions control computer to sleep. That sleep-mode disables the ability of the computer to on-the-fly adjust the fuel-air mixture ratio of the Carter BBD and to on-the-fly adjust ignition timing.
Ergo! No reduction of emissions.
Most web articles regarding the Nutter Bypass that I have read include a prominent disclaimer which explicitly states that the modification will cause the Jeep to be emissions illegal.
Configuration enforcement and emissions testing, however, are horses of other colors. From what I have gathered reading posts on the topic, emissions enforcement varies by state and sometimes by region within a state.
Who knows what you might get away with where you live?
Gadget