With the newest update you can use extra gained EXP and a new item gained from the exchange and commissions to increase the level cap for a ship.
Now what I am still trying to see is if it is based on stars or modification maxed. It did not help they used HAMMANN as the example who was both max star and fully modded. My guess is when you max out your stars and hit level 100 you can then start increasing the cap.
If you know more information please let me know so I can make a page relating to it here on the wikia. Thank you and good luck with your battles to come!