This is probably not a bug but my own stupidity. I created a world in 1.12 where spawn is no where near anybody of water in hopes that when it was updated into 1.13 snapshots or higher that new features would naturally spawn once the oceans were generated. Coral Reefs, underwater plants, and downed mobs spawn perfectly, and occasionally a small pack of Dolphins but other then that fish, squid or turtles do not spawn naturally. I recreated the world in 1.13 pre-release 3, as new world generation in pre-release 4 seems to be broken, to discover an abundance of fish. I'm hoping this is in fact a bug as I've spent months creating the original world for my server only to have one of the key features inaccessible naturally.
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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,
That actually might be whats happening! I have a large aquarium at spawn! I'll try killing the fish to see if that fixes anything.
This is still an issue in pre-release 7, but I guess im the only one with this issue. I've googled for countless fixes even trying /gamerule doMobSpawning true. If anyone knows of another trick I could try to attempt to get it to naturally spawn even squids would be great.