You can vault items by opening the character menu, pressing L3/Left Thumbstick/CTRL to enter vault mode, deposit the items like before by hovering over them and pressing the store button, and then to exit vault mode press the L3/Left Thumbstick/CTRL button again. Bungie are also considering feedback about keeping the change. Its being considered an issue, but it is also due to a change they made. For this specific thing rather than a reverting fix they may be looking down other routes such as keeping both systems in play and letting people choose the default via settings.