I think they're related, but unique creatures. Haunts whittle down children by presenting them with their fears to take possession of them. A Baku-Baku feeds off of fears of children (and adults) by causing them nightmares. They're both phobophages, but their modus operandis seem different. Haunts also seem to be a new type of creature that exclusively feed on children and can be seen by them (as hinted by Jim several times before when he's spoken about a potential young adult series).