The Rift and Quest stores serve different hardware and so show only the games relevant to that hardware. There are many games in common but certainly not all. Lots of people already complain about buying Rift games for their Quests by mistake - it would be much, much worse with a single combined store.
Which games (that you know exist on Quest) could you not find? When your Quest was connected to the PC, were you using Link or Airlink and viewing the store in the headset? If you were, you will have been looking at the Rift store, as the Quest is acting as a Rift in that situation, ie just a display device. You wonlt find any Quest games that way.