I’m a new user/purchaser of DT, and trying to understand the most productive uses of this powerful tool.  

A great advantage of DT is it’s ability to act as a freeform doc db; just drag it in.

However, (like many users, I’m sure) I have a legacy of deeply hierarchical folderized documents that I’d like to incorporate in DT.  Folders have multiple layers of sub-folders nested.

Does DT prefer a highly "grouped" collection of documents, or a more flat structure?  For example, are searches more or less efficient with a flat collection?  Does automatic categorization work better with deeply hierarchical groups?  etc.  Is there a general rule?

The hierarchy does not affect the performance but the deeper the hierarchy is and the smaller the groups are, the better the classification will work.

Usually a ratio of 1:10 or lower between groups and contents is recommended but in the end everything depends on the nature of the contents.