I have left several empty supers above a crown board as I have no storage space, and yes it can be a bit of a pain having to remove them if I want to feed with fondant, I usually take out a few central frames to accomodate for this, but stiil leave them in situ.
If it's above the crown board no worries, could be useful for holding insulation around fondant if you feed through the porter hole. The crown board is their ceiling, that defines their living area.