That's a tougher one to answer than it would be for changing out the headpipes, which is a definite emissions violation. We have to remember that emissions isn't just the amount of CO, NOx, and HC coming out of the system, there is also something called sound emissions that also have to meet standards. I'm not sure where you could get a 100% reliable and accurate answer to the question, but I'm pretty sure Harley isn't going to tell you it's OK. They would rather sell you their street legal higher flow exhaust system and street tuner.
As long as you don't change the tune, there won't be an electronic fingerprint to trip you up. But if someone at a dealership wanted to screw with you, they could easily tell the mufflers had been modified. What are the odds of that happening? I have no clue.
Ultimately, we all have to make our personal choices and then live with the consequences. Personally, I think I would take the chance on a muffler mod, but not the headpipe and catalyst. If it's really important to you to increase the sound level, you could always look for some take-off mufflers from one of the guys who changed out the system and install the new cores in those while keeping your stock mufflers stored. Then if you have a problem that requires a trip to the dealership, just swap the mufflers. Once the factory warranty is gone, and I assume the reason for your question is you value the warranty and don't want to throw it away, then you could do whatever you want.
JMHO - Jerry