Rules of pronunciation tend to mean less when Proper Nouns come into play. Largely, it's a matter of tradition. "Jacinto", as a Spanish word, means "hyacinth". If you were speaking about the flower, you would pronounce it [ha-SEEN-to]. However, in the context of "San Jacinto", the pronunciation becomes [juh-SIN-to].
Why? Because that was how the original settlers of that city pronounced it. The name became canonized, and remains in that (technically incorrect) pronunciation as a matter of tradition. That pronunciation became associated with that location, changing it could lead to confusion.
When it comes to names, you simply can't count on consistency of pronunciation. Why should Des Moines, IA, be pronounced [deh moyn], but Des Plaines, IL, is instead [des playnz]? Exact same situation.