Wood shakes are derived from rot-resistant tress like Redwood and Cedar. These trees contain alleopathic chemicals that seek to inhibit the growth of other living organisms. Rainwater run-off may challenge the growth of plants near the house. In my experience, I haven't observed noticeable differences in plant growth rate around redwood or cedar trees or boxes. The life-expectancy of a cedar roof is often between 30-40 years. If the shakes are treated and sealed, this can prolong their life. Consider the use of a silicone seal to waterproof the shakes.
Asphalt shingles are a petroleum-based product and a major source of pollution in rainwater runoff. It's horrifying to read the small print on some of these roofing packages that are asphalt based.
Pollution Prevention and Stormwater
Leaching of Heavy Metals from Stainless Steel