they cannot void your warranty. All they can do it not replace your shocks under warranty and they will say that it is because you put a spring in that has different specs from the OEM ones. They cannot say that they will not fix a leaking hose that is under warranty because you have aftermarket springs. Understand?
Now, if you put in an aftermarket intake and get an CEL, do not expect them to diagnose it for free without wanting to put in the oem stuff to make sure the aftermarket stuff is not the problem.