The answer to this question seems to be yes and no and yes and no. In #1, Jake-morphed-as-Homer mentions in his narration that Tom has a scent that is somehow subtly “off,” and I think the implication is supposed to be that Jake’s scenting the yeerk or some evidence of its presence. However, that idea never comes up again — probably because it’d make controllers pretty easy to detect, and K.A. Applegate is trying to tell a good tension-filled story — and there are actually moments in later books with people in wolf or dog morph being like “is this person a controller? No idea” (#16 and #19 both come to mind). So we’ll chalk that moment in #1 up to Tom having a dracon beam on his person, or spilling kandrona on his sleeve earlier that day, or just making an unfortunate choice in cologne that morning.
There’s also no evidence that Melissa Chapman’s cat (#2), William Roger Tennant’s cockatiels (#35), or Nora Robinette’s poodle-monster (#45) can detect anything alien about nearby humans’ scent or mannerisms or inflection. Jake and Marco morphed into dogs realize that the chee are odd for their lack of scent; real dogs themselves seem totally unbothered by this discrepancy (#10). Given how often real animals react strongly to unusual scents in this series (#14, #20, #39, etc.) I’m going to go ahead and say that the smell and sound and sight of human-controllers remains undetectable even to various animals’ better-than-human senses.
Then again, there’s the implication of the animals themselves having some non-conscious awareness on some level of “this human is off somehow.” It’d be sort of like Tobias talks about with his hawk side having a certain brutal pragmatism that allows its birdy little brain to accept even starvation and excruciating pain as reality — and his hawk side therefore being a hell of a better predator and flier than his human side will ever be able to think its way into being (#33). The hawk has no conceptualization of “why” or ability to put words to its experience, but the hawk knows on a level beyond consciousness about things like the yeerks’ truck ship (#3) and the hork-bajir valley (#23). Similarly, I think there’s room for the interpretation that some of the animals know on a level beyond consciousness that some of the human-controllers are somewhat off.
First of all, there’s the way that Homer and controller-Tom pretty openly dislike each other (#1, #9, #21). Sure, it might be partially because of real-Tom finding his kid brother’s loud furball annoying and the yeerk playing that part, but it also might be because of that sense of “something is not right about this human’s behavior, even if I don’t know what” that many pets definitely demonstrate if they spend most of their time around humans. As for what that offness actually looks like: we see the yeerks in both Chapmans be totally robotic when all they have to convince is a housecat and a 13-year-old girl, we see the yeerk inside William Roger Tennant go totally off the rails when apparently alone with his birds, and we get lots of other hints that controllers totally drop the human act when they think no one is watching. So the pets are probably not going “this human smells like an alien” but they might be on some level aware that there’s something unusual about any given human-controller, and also aware that they should be wary about that unusualness.
(Loosely-related tangent about biological motion below the cut.)
a LOT of dogs end up really defensive around human men, because they’re more likely to be abused— or witness abuse— by men. dogs learn to associate a whole gender with danger. in some cases they even go so far as discriminating between specific races. so, i bet a lot of dogs would end up looking for signs that a human is a controller, because if yeerks don’t even respect other sentient creatures, they’re damn well not going to treat companion animals well. a dog doesn’t have to be kicked or neglected very many times to learn that a certain smell or time of the week or facial expression— especially something as obvious as a lack of facial expression— means the human they’re with is going to hurt them.
also, like, i get that it’s something KA had to leave out for plot reasons, but if a dog can tell you ate a burger without them, or patted another dog on the way home, a dog can definitely tell that every three days you go down to a big pit full of aliens and weird liquid. dogs could 100% learn to tell if a human was a controller or not. there would probably actually be a lot of instances of controllers getting barked at and threatened by dogs who have learned that ‘kandrona smells are BAD NEWS’ from their owner’s friends or kids or coworkers or whatever. but humans are used to dogs just suddenly freaking out, so no one would ever just conclude ‘my dog has been abused by aliens and is trying to warn me’.
also, as another thought, i bet controllers can’t be zookeepers. not only would prey animals get super stressed by a caretaker suddenly treating them roughly and indifferently, if someone taking care of lions or wolves suddenly starts moving in a lame, halting, injured way… that’s gonna be a bad time.