I believe Brett was talking about link structure here, not as some seem to have assumed directory structure.
These are not the same thing. For example all the above categories could be at the same directory level - links do not have to follow directory structure. After all, how many users actually look closely at the page url?
I'm not suggesting everything should be at one directory level, but just to demonstrate the point you could have:
(Or if you want to preserve keywords you could have www.domain.com/coffee-beans/ and www.domain.com/coffee-farming/, etc.)
The link structure is imposed on the above by the indexes. To add a new category you just change an index, for example, to add Cup -> Tea -> India
To a user the above link structure is themed. However, whether a link structure which is different to a directory structure loses the benefits (if any) of a themed site in serps rankings, I have no idea...