For instance, in structure 2, does the 0 folder count as the main topic, and make google think 0 is the subject, or does the topic-name folder before it have just as much weight (and give it some bonus for being in the category, or would it be better to have the first structure with the topic name divided up, and with .0. ?
something like that... may not be right, but it's how I do it.
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Go the first one.
No particular reason, I don't think it makes much of a difference anyway.
With the first one your only 1 sub-folder past the root, with the second you are in 3 sub-folders where I think some sort of dilution can occur, or when it comes to visible PR being parsed anyway.. (for whatever that's worth.)