I agree. I feel that aftermarket intakes and exhausts should not void your warranty if they're installed properly, especially the exhausts.
Now I could see a dealer voiding a warranty on an engine related problem due to an aftermarket intake if they wanted to. They could get out of covering the cost of parts (and not making any money on labor) because they could say something like: "When you put a performance intake on a vehicle it has a bigger filter on it. In turn, you're going to have a higher rate of airflow, and with the higher rate of airflow you're going to have more dirt entering your engine, and the extra dirt entering the engine over time is what caused your engine problems. So we can't cover the engine under warranty."
Is that very likely to happen with an intake? Doubt it but it's not out of the realm of possibilities for a dickheaded dealership to pull that even if the intake is installed properly.