The darkness of the shakes is probably due to a combination of tannins concentrating on the surface, and mildew growth. (There also may be old stain contributing to the darkness.) So, in painting the shakes, the mildew should be treated first: apply a 3:1 mixture of water:household bleach, and allow it to remain on for about 20 minutes, adding more as it dries. It makes sense to do a section at a time, say 25 square feet.
After the 20 minutes, the surface should be rinsed by flushing with water. (Power washing with water is best avoided with old cedar shakes, as it can damage the wood.) Then the surface should be refreshed using a hand or power brush. The brushing action should be vertically downward, and done enough to remove the top layer of weathered wood fibers.
A steel wire brush is effective, but residual particles of steel can result in darkening spots in the wood. Thus, if a stiff steel brush is used, a new brush should be utilized (less likely to have bits of wire break off and discolor the wood), and the shakes then brushed off (vertically downward) with a stiff bristle brush. Alternatively, a heavy, very stiff natural bristle or plastic bristle brush can be used to prepare the surface.
Then an exterior stain-blocking wood primer should be applied. Options are: an oil-based primer or a latex primer. You and your painter will have to decide which approach to take. The oil-based type will have better stain-blocking capability for severely-staining shakes, but the latex primer will provide better long-term crack resistance, mildew resistance and general durability.
Applying two coats of latex primer will enhance stain blocking as well as crack resistance and mildew resistance. A quality latex paint can be applied to either type primer. An oil-based paint should be applied only to the oil-based primer. If you go with the latex primer, it is best to apply it only if the shakes are thoroughly dried out and the humidity is not particularly high, and not when it will rain within the next day or so.
Do not apply the primer in bright, direct sunshine. With the latex type primer, assuming two coats are applied, allow an overnight dry between coats. For the paint itself, we recommend using a top of the line exterior 100% acrylic latex house and trim paint in a flat or satin finish. Two coats will provide maximum mildew resistance, crack resistance and general longevity.