Just My Hapence, it depends on your Derech Halimud. You can go through the whole thing with the four elements and other ways of categorizing the creation. I would like to believe he did know Kabbala, simply because we know that other Geonim are part of the Shalsheles Kabbala and why would he stand out? However, I doubt Reb Shmuel ibn Chafni was a Mekubal.
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