Currently, with a 5 Wizard / 5 Pale Master - Magic Missile produces 5 missiles, which appears to be taking into account both Wizard and PM levels.
Isaac's Lesser Missile Storm also only produces 5 missiles, so it looks like this one isn't correctly taking into account the total caster level.
I don't have access to Greater Missile Storm, but I would imagine there's a chance it has the same issue.