In Oracle of Seasons/Ages, she only appears after specific, complex player actions.
In Skyward Sword, she is a childhood friend and reincarnation of the goddess Hylia, rather than a princess.
In Echoes of Wisdom, Princess Zelda is the primary playable character.
In games like Breath of the Wild, she is heavily featured in memories/backstory rather than in real-time action, a pattern seen throughout the series.
In summary, she is absent from a small number of entries.