Warranty doesn't become void for the whole car, only for the part you're replacing. If the aftermarket part is proven to have damaged another component of the car, then yes, the warranty on that damaged component would be void.
In the case of intake and exhaust, that's highly unlikely unless you damage something during install. No one has had any warranty issues with replacing. I myself have the Joe Z combo and did the install myself. I've brought my car in to the dealership for warranty issues and oil changes and an alignment and have had no questions asked.
What's your definition of "best"? Best performance gains for the money? Best sound?
For intakes, it's mostly just a sound thing. The K&N Typhoon intake is comically loud at WOT. But mostly normal when just driving around. So I absolutely love it.
The JoeZ intake is just a smoothed out intake tube. To me that's not worth any effort since you still have the stock airbox and stock filter. Either stay stock or add just a different air filter, or go short-ram.
Exhausts...the ISS has the dif exhaust tips and sounds awesome. The Joez/PTS has the deepest/best sound.