There are many reasons why it is not used.
First, it does not have the utility of Clefable. Clefable has RELIABLE recovery, as even though strength sap can heal a huge amount of HP against Special Attackers, which it specializes against. Because special attackers mostly run 0 Atk Ivs and an Attack Lowering nature, the recovery will not be that much. ON top of that, because of not always knowing what a Pokemon is running, is VERY unreliable. Clefable, has soft boiled, however, which is always a constant 50% recovery. On top of that, Clefable has a MUCH better ability than Shiinotic, being Magic Guard. While effect spore is a decent ability, being able to not take hazard and toxic damage is excellent.
Grass Fairy is a horrible defensive type. While it does have 6 resistances, it has NASTY weaknesses to Fire, Ice, Poison, Steel and Flying. The four times poison weakness is horrible. Clefable has weaknesses to steel and poison, and while it doesn't have that many resistances, it has a lot of neutral damage.
Shiinotic also has low defense and lower HP, which are not traits that clefable has. While Clefable, doesn't have the best defense, it has good HP and good special defense. Clefable can even use wish with its high HP to heal a battered sweeper that the opposing team barely hung on from. It can set rocks, it can take away items, it can do a huge amount of things.