What does "all" mean here? and would the meaning be changed if I say "can we all just go back"?
"All" means everyone. Merlin is asking Nemo if Nemo, Dory, and he can go back to bed. As for the second part of your question, the meaning changes slightly if you only say "Can we all just go back?" This means that you want to go back home or to a place you were previously; it no longer means that you would want to go back to sleep. "Can we all just go back" is perfectly fine to use and is used often, it's just not specifying a particular place or location. Here are some examples of "all" being used. Ex: Why don't we all just go back inside? It's quite cold out here. Ex: You all are in big trouble! Ex: Let's all go to the beach today!