Model cement works on the principle of melting the plastics together to form a bond. Super glue is a brittle, yet strong chemical bond. If you think about it in terms of layers you’ll see what happens. (plastic-paint-glue-paint-plastic) Your bond will only be as strong as the bond of the paint on the plastic. The superglue may react or mix with the paint, depending on the type of paint you are using, and this will affect the bond strength.
Bottom line: Gluing painted pieces together is not a wise idea, if you want a strong bond.