Will an old (13 years) german shepherd be aggressive or protective to a small dog?

It sounds doubtful, since you have already observed he isn't good with other animals. How a dog is socialized during it's first 3-4 months of life, the critical socialization period pretty much sets that dog's personality for life. Some dogs like and are tolerant of puppies and some are not.

I recommend you test your dog, in a safe way with the puppy before bringing it home and then carefully and gradually introduce the two.

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