Honey is ok for puppies in reasonable amounts, 1-2 cc should be well tolerated by a small puppy. It is often used as a quick energy source to deal with hypoglycemia. As for the cough, there is no reason not to try honey to soothe her throat. Many veterinarians would choose to start the puppy on an antibiotic and I also prefer the use of an expectorant. Use of a nebulizer or humidifier is another great way to soothe and moisturize the upper airways. Take a look at the three videos about respiratory disease and also the one on "kennel cough."