If a Shedinja is in the rain, Fire attacks are no longer super effective. Will it hit it, or no?
Effect: Increases the power of Water-type moves by 50%. Decreases the power of Fire-type moves by 50%.
-Bulbapedia
So the super effectiveness of Fire does not go away, it just hits like normal effectiveness.
It will still hit because in the rain, fire attacks are still fire attacks. They just lose power.
Fire is still super-effective even in Rain so it will hit