It's a problem with AIs across the 4X spectrum in Civ6 some city-states spam Scouts, I bet if you look at the ships of one of the other races they are either spamming one type of Warship or like in my current game Asteroid Miners.
At least spamming colonies can actually help the AI, having 50 or 60 Asteroid Miners and 4 asteroids and not having "invented" the Slip Stream? tech, while being at war, not so much.
One way to stop the AI from having dozens of ships it can not use would be to have it value Treasure or Tech Fleets more.