While it's slightly less serious or complex than movies like The Da Vinci Code, and it isn't all about religious symbols, National Treasure utilizes puzzles and clues in the same way for a quest that's about secrets from US history and even involves the Knights Templar, as The Da Vinci Code does.
The Priory of Sion hid her identity to protect her from possible threats to her life. The real meaning of the last message is that the Grail is buried beneath the small pyramid directly below La Pyramide Inverse, the inverted glass pyramid of the Louvre. It also lies beneath the "Rose Line," an allusion to "Rosslyn."