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In order to void the warranty, the MOCO must PROVE that any changes made caused the problem being looked at. That is hard to do. "Mufflers" shouldn't void your warranty. Changing out the entire exhaust system could cause problems if there is an issue due to 02 sensors or something being out of whack. The dealer installing them probably won't make that kind of error though.
Tuners can be a different story. If you're worried about it, and not looking to really boost performance much above stock, just get the dealer download to the ecm and you should be golden.
7 Surprising Harley-Davidson Products that Are Not Motorcycles
Slideshow: The bar-and-shield logo shows up on far more than motorcycles, some of the company's most unexpected products have nothing to do with riding.
Slideshow: From the troubled AMF years to modern misfires, these bikes earned reputations for reliability issues, questionable engineering, or disappointing performance.
Crazy Bunderbike Build Looks Amazing, But Is It Impossible to Ride?
Slideshow: The Swiss custom shop has taken a Harley Softail and stretched it into something so long and low that it looks closer to a rolling sculpture than a conventional motorcycle.
Engraved Rebellion: Inside Bundnerbike's Glam Rock II
Slideshow: A standard cruiser becomes an intricate metal canvas in the hands of a Swiss custom house known for pushing Harley-Davidson platforms far beyond their factory brief.