I've also had the problem of squid and fish mobs not naturally spawning on my multiplayer server (I could still find dolphins and turtles because I don't think they despawn and they were spawned before I started experiencing this), but I was able to get them to spawn again today by moving the world spawn point to a further away area. In my case I think it had something to do with a large aquarium we made near the world spawn point, and since chunks near the world spawn point stay loaded no matter where you are on the map, it may have thought it had reached the aquatic passive mob cap no matter where I was so it didn't spawn any of them. Try setting the world spawn point in a few far off places and see if it can get the aquatic mobs to naturally spawn again,
I've also had the problem of squid and fish mobs not naturally spawning on my multiplayer server (I could still find dolphins and turtles because I don't think they despawn and they were spawned before I started experiencing this), but I was able to get them to spawn again today by moving the world spawn point to a further away area. In my case I think it had something to do with a large aquarium we made near the world spawn point, and since chunks near the world spawn point stay loaded no matter where you are on the map, it may have thought it had reached the aquatic passive mob cap no matter where I was so it didn't spawn any of them. Try setting the world spawn point in a few far off places and see if it can get the aquatic mobs to naturally spawn again,