I still think it's possible that Mavra was behind the pupnappings. She was in town and had darkhounds with her. I like to think that she would enthrall them and build a new Blamp wizard corps, each with their own dark temple dog.
But with it confirmed that two were taken, rather than more, it does seem likely that they're with Cowl and Kumori.
Minor note: I think there was a minor editing mistake. I think Maggie at one point said Harry was only wearing a t-shirt and jeans and didn't have his duster, but Mouse later observed her tugging on his coat sleeve. I don't have the book handy and I only read it once, so I may be wrong
Mouse's section was such an amazing intersection of hilarious and adorable and so fundamentally Dog that it had me on the verge of tears.
It reminded me of Rowl's scenes in The Aeronaut's Windlass. Which was my favorite part.