Please, please, please let the owner know. You will be surprised at how much an owner is left "unaware" about certain things, like this and just plain customer service. Call and ask to speak the the owner. This is what I would say, maybe help give you an idea.
"I was in your store the other day and I was looking at the baby ducks and chicks. I noticed there were a few dead, when I mentioned this to your employees they were very VERY rude to me and would not remove the dead animals from the pens. I think you need to speak with your employees about customer service, general manners, and how to PROPERLY care for the animals. What I saw the other day in your store was very very saddening and it reflects very very poorly on you, the owner. I am not the only one who thinks this, there are many other people who have file and talk about these same complaints. I just thought you the owner would like to know what people think of your store because of these events. Thank you and have a good afternoon."
That's all I would say. Like I mentioned before, many times owners are not aware of everything that goes on in their store, no matter how much they would like to know everything. You do not have to give your name or number or anything like that.
Good job reporting them to the humane society, talking directly to the owner would only further encourage the store to take action.
-Kim