open the console, click the item and write disable
note:this only works if the object is on the ground, so I recommend deleting any mod-related objects before you delete the meshes, textures, etc and .esp
(I don't understand why you still have the item if you deleted the mod though)
I would use "set delete 1" or is it "set delete to 1" ? I think it's the first. Disabling things still leaves the reference there, deleting removes it.