Fireball is not the only spell in their arsenal.
Doesn't matter. They're still limited to the same number of slots per level.
Also they don't need many spells to take down enemy ships.
Only if there are no counters to those spells. And since there are counters to spells in regular combat, why would there not be counters to spells in naval combat?
They can also freeze, shock and the rest. Lightning damage also lights wood on fire.
Magic could also shield against such attacks, put out fires, and so on and so forth.
Only situations where you will lose to cannons is if enemy outnumbers you greatly but in that case you needed more ships in the first place.
You can put a lot of cannons on one ship. You could put a lot of mages too, but are mages that common?
Basically, your argument boils down to, "If magic can do the same thing as artillery but more easily and more effectively, then artillery doesn't make sense in a setting." Which is quite true, but in the case of Pillars, your premise doesn't hold: we have no evidence of magic that operates over the kind of range you'd need in naval engagements, the number of casts is severely limited, and a fireball is nowhere
near as powerful as a broadside. It's about as effective as a small-arms volley from six combatants.
i.e. your hate-boner is blocking your view again