I've seen it all of my life but never gave it much thought.
You'll find IHS on Greek icons, where it stands for the first 3 letter of Jesus' name in Greek, IHSOUS-- Iota Eta Sigma, which in our (Latin) lettering looks like IHS.
It's also reportedly carved in the wall in some of the catacombs under the city of Rome, where it's not certain if these were Latin-speaking or Greek-speaking Christians. If Latin, it is thought to mean Iesus Humanum Salvator (Jesus Savior of Mankind) or In Hoc Signum ("in this sign," i.e. the Cross.)
The Church has no problem with multi-meaning symbols. In fact, uses them all the time.