flying/animate weapon doesnt target and therefore doesnt check whether you have a weapon in your weapon slot or not. it is a unique ability that will simply replace a weapon with a creature version of that weapon (does not count towards destroy or steal which is why it can affect morning star/glory, protected weapons)
if you dont have a weapon, the spell will still resolve, but no weapon-turned-creature will be created, as is the case if you have a full creature slots. the weapon will simply vanish
think of it as a 'global' spell somewhat similar to Rain Of Fire / Plague / Pandemonium