A lot of the components of the vault of glass are incorporated in normal gameplay whether you do strikes, dailies or just tool around some of the planets. That said, i think we will see the witches spawning those green circles that kill you during the second bridge section and during the deathsinger's song portion. Maybe in the abyss as well. I also think that during crota's end we will encounter the gaze randomly and more often then just when someone dies. More, bigger, badder nasties.