Good point. I don’t disagree. Manually tagging (and filing) will probably result in more meaningful organization, as there’s abstract and abductive things your brain can do that the computer simply can’t.
That said, tags—even programmatically generated ones—offer a couple of things that are above and beyond the queries you describe. One is browsing. It’s cognitively easier to look at a set of tags as cues as you’re looking for something and to click one than to generate a query for the same set of features represented by that tag. Instead of a tag, though, this could be implemented through some kind of saved smart search.
The second isn’t really related, but worth mentioning (even though it’s obvious)—a file can’t really be in multiple subfolders (with exceptions, e.g., aliases in Finder and replicants in DT) but it can have multiple tags.
But yes, in general, manually organizing stuff is probably better if you’re willing to put in the effort. (I am not. 
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