It won't void your warranty, but any problems you have because of the
flowmaster exhaust or its installation won't be covered.

Be sure not to remove or modify your catalytic converters.  Besides being
highly illegal, I *have* seen converter tampering cause Hyundai to
threaten to void a warranty.

Also consider that a significant amount of the restriction in your exhaust
is the catalytic converters.  I wouldn't expect a noticeable increase in
power or fuel economy.