It seems unreasonable that it would be for genetics that they don't like dogs, especially for a species that are masters of genetic engineering.
Most of the traits you and others have listed for why people may dislike dogs are things that humans have already worked around... we have hypoallergenic breeds, quiet breeds, docile breeds, etc... while it takes a lot of time and desire to breed a species the way we have with dogs, it would be world breaking to me to just say it's because of their genes. Most readers will be able to see what reality has achieved with dogs and the idea that dogs are genetically 'bad' or unworkable will shatter suspension of disbelief.
I think you're more on course by looking at reasons people don't like dogs: they smell, they're dangerous, they're predators. This also gives you lots of room to world build and develop your Pandemoniums(?) and their culture. Consider other reasons that people don't like dogs, and also consider things that dog lovers dislike about dogs, and find ways to build out the culture of Pandemonium around these traits.
You've already established that they're noisy and smelly. Do you know why? Dogs are pursuit predators. They use their odor and noise to scare prey and control the direction that the prey flees so they can drive the prey into other packmates or dead ends. Wolves will take turns making noise once they've cornered prey to keep the prey from resting and in a state of constant fear, which is very draining. They do this until the prey is thoroughly exhausted, and then they strike when it's weak. There's a lot of cultural baggage you could unpack from there, based on the culture and environment. Maybe Pandemonium has other, larger apex predators and so stealth is of the utmost importance. Maybe Pandemoniums developed a culture around solo combat and pitting one's strength against challenges to prove one's worth and so see pursuit predation and pack tactics as cowardly.
You use some very nebulous terms like "good pets", but that's incredibly subjective, even in reality. I'm a dog person. I have known people who hated my pets, but enjoyed lizards. Lizards mostly just sit in a terrarium under a lamp. You don't really interact with them much. These people find this ideal as they value independence and cleanliness: the lizard needs minimal interaction and it's mess stays within it's terrarium. Conversely, dogs require attention. They are pack animals and without regular social interaction, they suffer. Most "bad dogs" that you hear about (violent, obnoxious, ill behaved) suffer from not getting their social and mental needs met. My dogs require attention and exercise daily. I have to schedule my life around being able to return home to let them outside to do their business, and I can't go more than a day or two without taking them on a long walk or half an hour of fetch in the yard. These are things that are intrinsic to dogs as social animals and would be extremely hard to breed out. It is possible... there are more independent breeds (like Shiba Inu), though they will never be the sort you could put in a terrarium and ignore. Thus, the lifestyle of Pandemonium could greatly affect the compatibility. Long hours in a lab without interruption, or multi-day trips way from home would both strongly discourage dog ownership.
On the other hand, one of the biggest things that dog lovers (and cat lovers, honestly) hate about their pets is their lifespan: dogs live between 8 and 16 years, depending on breed and size. The bigger the dog, the shorter the lifespan (generally speaking) and wild wolves have even shorter lifespans due to injury and competition and lack of healthcare. Cats are more on the order of 16 - 20. There are exceptions, but 90% of the species falls in this range. Humans are much longer lived. This is one of the cruelest aspects of having dogs or cats, that it feels like just as you're starting to get to know them, have them trained how you like... they die. This is a thing that could maybe be enhanced with advanced genetic science, but it would be after thousands of years of association. Their lifespan isn't such that they just break one day, either, they decline slowly with time. Most dogs will peak around 5 years of age, and begin to decline. Past 10, they slow down and start to struggle. The last few years of an animal's life, if you're a responsible owner, is often spent caring for them in declining health. This involves watching your friend break down, and usually involves all manner of unpleasant smells and bodily fluids and culminates in heartbreak. I begrudge no one who looks at that and says "I think i'll take a lizard thank you". Other pets like birds and lizards have better lifespans. African Grey Parrots often need to be written into wills as they regularly outlive their owners. It would not be difficult to create a culture that views this and thinks, "ha, how weak and feeble," though do expect that this would make most readers react negatively (so, great if you want people to find them somewhat arrogant or villianous).
Another challenge of dogs, one that is a harsh reality not often discussed in survival fiction, is feeding them. Cats and dogs both are carnivores. Dogs are more omnivorous (and this is a highly contentious topic that often starts arguments), but the mutations (specifically the AMY2B gene) that enhance real world dogs ability to process carbohydrates (via the enzyme amylase) is something that differentiates them from wolves and likely evolved from living with humans and eating our left overs. As such, depending on the food practices and preferences of Pandemonium, carnivorous pets might be challenging to keep or even morally offensive. We don't know enough about them culturally to say, but if their diet is based more on vegetables, nuts, and seeds.. then a dog (especially a more wolf like dog) would be very challenging to keep fed.