Yes, this tale does have a very strong vegan message. As the witch and her cat learn more about the clams and interact with them, they realize that the clams are living beings, too. More than that, they are fast becoming friends. You don't eat friends.
I loved that the witch (and her cat!) grew throughout the story and opened themselves to love and service to others, and became much happier beings for it.
Message books can be kind of preachy, but I really didn't find this one to be overly so. Nowhere does the author explicitly state that eating meat is bad, or even that you should want to help others in order to be a decent human being. Things just unfold naturally in the storyline.
As a vegetarian venturing into veganism myself, though, I love having this resource to begin to talk with my kids about the ethics of food choices. (My children are six and two.)