The Habakkuk is an Superweapon and their hull is made of ice (like an iceberg).
The ice hull makes it fast repairable and thus really resistant to damage.
It's also an Aircraft Carrier witch makes it an bit more hard to defeat. Beside its aircraft, cannon, missile and energy-based ordnance is available for this ship
To defeat it, a contiuous attack combined with flame based weaponry makes a good account of it. Beware that it will continously repair itself. Combined with enviromentall effect of suddent blizzard around it, a direct attack would be challenging. Fortunatelly it is an optional superweapon available only if a certain storypath is taken and thus can be avoided if another storypath is taken.
The Habakkuk may be based on cancelled real world British project on the very same type of hull, with the very same name : Project Habakkuk, intending to create an unsinkable aircraft carrier made from ice. The project was aborted as it is considered unpractical and technologically flawed.
See also: Superweapons