This is common practice with shelters, since it is pretty much impossible to enforce spay and neuter after adoption. In my experience younger dogs seem to handle it better and heal in no time. I don't think there is more complication with these S/N than in adults. I fostered countless dogs, and never had incontinence issues because of spay. On the other hand most vets will not do elective surgery on an animal whose breathing is compromised. It sounds like mild kennel cough, very common. Your vet will probably send her home and do the surgery after it clears.