It makes since that Cruella would be Roger's number one suspect after the puppies are stolen. She had tried to buy them several weeks earlier and she was very obviously angry when she was told they weren't for sale. In fact, when she leaves them her words imply that she is already plotting revenge.
You could chalk up Cruella's lack of concern for the cold while tracking the puppies with Horace and Jasper to just being as determined to get them as she clearly is, but she's also the one wearing a likely thick and warm fur coat, hat, and with gloves, whereas Horace and Jasper are somewhat bundled up, but probably are not as covered as Cruella was.
Consider the scene where Cruella barges into the Radcliffe's flat just minutes after the puppies were born. It wasn't just good timing on Cruella's part—we can see later on that Jasper and Horace were spying on their flat the whole time. Cruella was outright stalking the Radcliffe's for their pups.
We know that Cruella and Anita are old friends, and Perdita reacts in horror when Cruella comes to visit the flat, hiding under an oven. Considering that she probably is familiar with Cruella, and given what we know about the Devil Woman, what exactly has she done in the past that would get this reaction from Perdita?
For bonus horror, the live action remake establishes Anita as a Mama Bear who will knock six bells out of anyone who she thinks wants to harm or kidnap her dog. Combine this with the above and what we know about Cruella's and Anita's relationship in the present, the most likely outcome is that Perdita got separated from Anita at some point, and Cruella took the chance to harm her out of sight. Anita only saw the aftermath and became violently protective of Perdita from then on, never knowing the one who hurt her dog was the one she called a friend.
One has to wonder if Dipstick's low intelligence might be the result of that flea infestation cutting off a lot of blood to his brain. Then again, a dog having that many fleas is disturbing in itself.
