Good point. I missed this when I first left Java, because in Java you get these nice classes. Over time I've found I use class structures a lot less, or in some situations I'll hack them. The other day I was writing a tree builder where in java I would have had a different class for "node", "attribute", etc, all extending from element. In my python impl I just had a class "element" with a string field "e_type" which was "attribute", "node", etc and then I stuck other stuff into a dictionary in that object as I needed it. Over time I've found that the extreme brevity improvements combined with blocks of documentation to describe the purpose of a grouping of code more than make up for the loss of code-based structure.
Again on the topic of organisation of data - in databases you get a lot of automatic documentation because the schema abstraction we're used to is so widespread and accepted. This is one of the reasons I love to stick with relational databases even though I know that there are good arguments, particularly in FP communities, advocating more practical forms of datastore.