I would say no ill effect on the injectors - it is actually less wear and tear on the injector to delivery more fuel via a higher flow nozzle than to increase the injector duration via a tuner / programmer to accomplish the same thing. The same applies to the CP3 - the alternative to a higher-flow nozzle would be a tuner / programmer and if that increases rail pressure there will in turn be more wear and tear on the pump.

2013? I must have missed something - original question referenced a 2003......