Cedar shake siding should not be painted. If they are painted, re-painting will virtually destroy them as shakes are too thin to withstand the preparation process.
Solid stain is the ideal product for cedar shake siding. Stain requires little preparation as it does not chip or peel. Primer should be avoided on cedar shake as it blocks the stain from penetrating and bonding with the substrate.
Aesthetically, the Semi-transparent stain is ideal but it requires a high maintenance. Semi-transparent stain requires power washing and reapplication every 2-4 years depending on UV and moisture exposure.