Far as I know, it's only ever been Kronos in canon. Qo'nos seems to only be a thing in novels, video games and the like. For whatever reason, fans seem to have latched onto it as well.
I have observed the same. In all the movies/shows I have watched with close-captioning, they say "Kronos".
It seems to be pronounced that way to.
But in the novels/video games/comic books, it's Qo'NoS.
I think I'm gonna go with "Kronos". Definitely more canon.