Because they were not even a little bit good
The Legend of Zelda is regarded as one of the best franchises in gaming, but there are some black sheep in the family. Specifically, the Phillips CD-i titles Link: Faces of Evil and Zelda: The Wand of Gamelon are held as embarrassing black eyes on the franchise, as they are ridiculously terrible. In fact, some people find it easier to disassociate Zelda with the CD-i installments altogether.
One such person is Legend of Zelda director Eiji Aonuma. Speaking with MTV Multiplayer, Aonuma did his best to distance Nintendo and Zelda from those titles. He remarked that Nintendo doesn't consider the CD-i projects to be part of the Zelda canon, and that "they don't really fit in."
It's rare that a Nintendo employee would comment on these games, as the company has typically remained mum on the topic. However, their blatant omission from the Hyrule Historia book probably says more than enough about how Nintendo really feels about their existence.
Eiji Aonuma Addresses Those Horrible 'Zelda' CD-i Games [MTV Multiplayer]