The explosion of Amazon and other online retailers made the advantages of clamshell packaging moot. However if you are a manufacturer, it may not be economically feasible to produce two different types of packaging for different retailers so lowest common denominator wins out.
Amazon has tried to combat clamshell packaging[1] with a few manufacturers (Fisher-Price, Mattel, Microsoft), but it has yet to be adopted by the rest of the manufacturing industry.
[1]: http://bits.blogs.nytimes.com/2008/11/03/amazoncom-cuts-pack...