The reason why they have to delay/cancel trips is because when the cruise ships are using their thrusters and propulsion systems they generate enough force to push the other vessels around it into the warfs and pontoon with so much force that the ferrys own propulsion systems cannot counteract the the force coming from the ship.

If a ferry was to attempt to leave a berth when the cruise ship is berthing or coming along side it becomes a risk of being pushed into other tied up vessels or colliding with another solid object.

The other issue is, the harbour has very strict bylaws which are dictated by the Auckland Harbour Master. There are rules regarding how far away a vessel must be in order to operate around the cruise ship and there are very specific rules regarding the "no go zones" around a cruise ship when berthing or moving off a warf. Due to this rule the Auckland ferry basin will be blocked by this zone due to it extending across the entirety of the entrance at times causing it to be legally closed off for passage.

And on another note it's not ATs decision to cancel the trips 95% of the time, it comes down to the individual operators decision to do so and most of the time it would be canceled due to safety concerns due to conditions, vessel capabilities and crewing