It's not a miss chance; it's a 50% chance to ignore damage.
Even when struck by magic or magic weapons, an incorporeal creature has a 50% chance to ignore any damage from a corporeal source—except for a force effect or damage dealt by a ghost touch weapon.
So a spell that does not require an attack roll, but deals damage, the creature has a 50% chance to ignore.
A spell that requires an attack roll (or not), but does not deal damage, the creature cannot ignore.