Bongo Bongo is Named After Rongorongo

Bongo Bongo’s name is probably derived from “rongorongo”, the name of a currently undeciphered script developed on Rapa Nui (also known as "Easter Island"). It's notable in anthropology for probably being a rare instance of a written language being developed independently of any others. However, the script's status as a "lost civilization" mystery also led to its association with the paranormal in popular culture, including in Japan. I recently became aware of the popular 1990s TV show Night Head, which exemplifies this association: the show's intro features rongorongo as a vague signifier the paranormal / unexplained, largely disconnected from any historical context. (By the way, this show is also referenced a lot in Pokémon Red / Green / Blue / Yellow: see this post and this video for details.)

Starting with a vague prompt to create some kind of paranormal boss enemy, the designer of Bongo Bongo, Takizawa Satoru, may have had “rongorongo” come to mind and altered it to reference bongos to fit the music theme of Ocarina of Time. Thus, the visual design of the boss would have come after the name, which would explain why the bongo association isn’t really explained and the battle taking place on a giant bongo doesn’t actually affect much (although, to be fair, wearing the hover boots does cancel its effects, so there is some logic to the design).