It has nothing to do with Kythe.
I'm on the Kythe team, and I don't know off the top of my head what Zoekt is. Looking it up, I see it's some sort of trigram search, which means if it's used at all (I have no idea), it's codesearch proper, not Kythe.
The Kythe index is the semantic index of the codebase, Codesearch does all of the text/regex/etc searching.