Lag> The hovercrafts TRANSMIT the access-codes to Zion when they're on approach (hence the reason the crew onboard the Hammer were in big trouble when the sentinels tore the radio off in Revolutions).
The Machines would be able to "cheat" Zion to get them to open the gates, thereby giving the sentinels access to the city and be able to shut down light, air, defences.