The games are too different for Zero Hour to be a N64 version of Time to Kill. The similarities end after "Third-person shooter Duke Nukem game with a time travel plot." And even then the time travel itself is different, with Time to Kill's plot being that an alien race called Draks are muckin' about through Earth's timeline in an attempt to kill Duke, who just hops through time to kill them all.
In Zero Hour, Duke gets a message from his future self (who had time-traveled to the past and sent the message from that time period) that aliens (the same ones from Duke 3D,
under new leadership) are attempting to rewrite human history and wipe out mankind. Duke attempts to destroy the alien's time machine inside the Statue of Liberty but is instead sent to the post-apocalyptic future. There, Duke meets up with a human resistance and uses their time machine to go back to various points in time and wipe out the aliens causing trouble in each time period.
Past that almost every other mechanic in the game is different, even movement, aiming, and jumping.