I would think this is a largely personal approach and could even be a hybrid using each kind of reference (and could also contain links to concepts like grace, Jesus, sanctification, etc.).
“Studying the Bible” is an extremely vague concept. An atheist with an interest in literature will no doubt approach the study of the Bible in a very different way from a priest who is looking for religious enlightenment. There is no “right” way of doing it. Any way that works for the end purpose that you have in mind should be good enough. And you can always change it if it isn’t working.
I’m asking because Zettelkasten isn’t anything more than one specific way of organizing and note taking. It’s not for everyone and it’s not the pinnacle of those actions.
Use it if it makes sense to you; don’t if it doesn’t