The Conventional Wisdom
Everyone knows that skunking is caused by light, and that clear bottles and sunny fermenters can cause off flavors in beer. For this reason, many homebrewers are concerned if hops are packaged in clear bags or jars or stored in a brightly lit case. Probably as a result, hops are often stored in dark freezers in opaque or translucent bags.
It is pretty clear that light causes skunking, and it is widely known that hops are the culprit. But on the other hand, hops are a plant, and spend most of their lives in the sun. Is it really important to store them away from light after they have been picked?
Dave Wills of Freshops answered this question on the June 1, 2006 episode of Basic Brewing Radio. He confirmed that skunking is the result of light interacting with isomerized alpha acids, which do not exist in the raw hop products (including hop pellets and hop plugs), but are created in the boil. Sunlight may cause some discoloration of the hops, especially noticeable in whole hops, but will not affect the flavor. The main factors affecting hop freshness are storage temperature and oxygen; see the article on Storing hops for more information.