The Aquila can be upgraded to accommodate more guns, a wider variety of ammo and reinforce the hull. To completely upgrade her costs: 104,500.
There is an achievement/trophy for the first upgrade and for completely upgrading the ship.
Wooden Hull Reinforcements: 13,000
Iron Hull Reinforcements: 25,000
Naval Ram: 8,000
Improved Rudder: 11,000
Extra Cannon: 2,500
Heat Shot: 19,000
Grape Shot: 17,000
Piercing Round: 9,000