Shake roofs have been around for centuries and are one of the original roofing materials. One issue with shake roofs that were installed in the last 30 years is the installation itself. Lath installation is no longer used and they are now installed upon decking with an underlining, or what we call roof felt.
There is a layer of interply roofing felt installed under the shake. That felt is not design to be exposed to the elements. When shakes age, some will check or crack. If they do, some felt will be exposed and will deteriorate to the point where the roof decking will be seen. Bare roof decking is problematic, and will lead to a lick entry point.
Over time, the shakes lose their integrity, which can lead to interior water damage and premature roof replacement if there is no regular roof maintenance or cleaning.
Many shake roof homeowners were never told they need to maintain their roof in order for their roof to reach its potential natural lifespan of anywhere from 40-60 years. Normally after a 10-year period of not cleaning, a homeowner will notice the green moss or mold, the lichen or the dark brown to black coloration of fungi.
At this point, many homeowners believe that a new roof is needed, when in reality, regular maintenance to remove and replace the deficient shakes and a good cleaning will keep damage from occurring and will allow the shakes to breathe and stay dry.
In regards to staining and sealing a shake roof, staining is fine for curb appeal but adds no real value to preserving the roof itself. Sealing a shake roof should never be done as this will keep the shakes from getting the air they need to stay dry.
In addition to cleaning, you should make sure there is no debris left in the valleys and no trees hanging over the roof, as this will cause moisture and shade. Also, it is a good idea to replace missing shakes and checked (cracked), loose or missing ridge caps that expose the inter-ply felt, as UV light can cause felt deterioration.
The best way to prevent leak damage is to maintain the roof on a regular basis, and if you have a leak, call a professional roofer.