The franchise did loosen up religious references a little bit starting with Star Trek: The Next Generation and featured more imagery and information on alien religions, but the Federation itself has always been pretty secular.
Season 2 of Star Trek: Discovery possibly having some sort of religious theme is an interesting decision, considering the franchise’s creator Gene Roddenberry was an atheist.
With that in mind, whatever exploration Star Trek: Discovery does of these themes, one would imagine it won’t play out well for the spirituality side of things.
Religion did not find its way into Star Trek plots often, and when it did, science usually prevailed over any spirituality.