It likely wont kill her to get a second rabies shot, especially if it is the one year not the 3 year, as you said shelters error on the side of caution and just vaccinate all intakes if they don't know the history. However it does increase the likelihood of things like, vomiting, diarrhea, loss of appetite, lethargy, and seizures, as well as over vaccinating increases the risk of injection site cancers.