Now You See Me
Though we never actually see one in the book, wolves are the subject of an awful lot of talk in Revenge of the Witch. The Spook apparently has a sharp nose and a beard like a brindled pelt, so he reminds Tom of a wolf. At one point, in the dark, Tom thinks the Spook's voice "sounded different, sort of deeper and strange. I imagined him on all fours by now, wolf hair covering his face, his teeth growing longer" (4.19).
Werewolves are never disproved in this world, but that doesn't mean the Spook is one. Maybe he just wants to look like Joaquin Phoenix.
Or maybe Tom is just being paranoid.
Now You Don't
Tom sees wolves everywhere. He asks the Spook if there are any wolves in a region called Wolf Fell. He thinks the human thugs in town are "staring at [him] with hungry faces, like a pack of wolves" (6.47). And, when the baby goes missing, everyone wonders if it could be wolves.
Perhaps there are real wolves that appear later on in this series. Or maybe Tom's latent fears of the unknown are just manifesting themselves as hairy four-legged beasts. Either way, the wolves in this book definitely represent Tom's anxieties about what he does not (yet) understand. We've read Little Red Riding Hood, so we with Tom on this one.