I have seen creepers, spiders and sheep vanish in the distance whilst playing. I wouldn't spend so much effort on getting the squids into the aquarium. I believe that all spawned creatures have a limited lifetime. All you can do is try and make ideal scenarios for them to spawn them in. You can't expect them to "stay alive".
That is where the dogs are/will be different because they have a health bar that can be maintained by players and don't have a limited lifetime.