Installing a shower flange in a subfloor
It probably doesn't matter much one way or the other since it's unlikely for water to get that far. I personally would not bother. Consider this: If water were to get that far, you would want to know about this and take action. If it's sealed, water could just sit there unnoticed, rotting out anything it touches.

If it leaked down and stained the ceiling, you would notice fairly soon and take measures to stop it. Stained drywall ceiling is way more easier to repair than a rotted subfloor.