Waterlungs, Underwater Movement and a Hues/Shadow type spell would make the mage nearly undetectable.
Castle and Ruins has some great spell list used to place protections during construction of a building. These could easily be used on ships too, which are floating and mobile buildings.
I also use living ships, grown using Animist magic with ritual and spell mastery. These ships can repair themselves over time, have plant growth spells used to heal them quickly(even imbed the spell as a daily spell at the helm, in an item owned by the captain/firtst mate/etc), can grow sails or oars and of course resist magic at the level of the "plant". Spirit of the ship, or even spirits tied to the ship via magic, are also very handy defenses (refer to Essence Companion).
Faillng that: yes a mid level sorceror could destroy a modern day aircraft carrier. But if such ships always had a platoon of Beast Masters on board with bonded sea creatures following under and around the ship, spell users will have obstacles to deal with. Even a low level cleric can summon a low level megladon. I say your best bet if more detail in your cultures, and failing that, a table to roll on that helps you determine the strength of defenses present, including none but a lowly lookout.