I've got some bad news for you buddy. Squid don't spawn 'wherever there's water' like they used to, they only spawn in the ocean and rivers now. All land-based squid farms are broken.
: Maybe Brad could work his biome magic on the trap before we upgrade? If we keep the same seed it'll pretty much stay the same in the southern chunk.
Old ocean chunks should get cod and (probably) Drowned. I don't think kelp and seagrass will generate - most likely have to plant those manually if you want the new look. Not sure about temperature... I'm guessing they just stay mid-temp? If they get colder or warmer we'll get extra fish/dolphins depending on which way they go.