So assuming we all agree that Vintage is not really a one-deck format, there are a few possible explanations for the above data:
The format's best players play Shops, and its worst play decks that prey on Shops, so that the win percentage of Shops against its predators is not accurately reflected in tournament results;
Even though Shops as a whole has a winning match percentage against all other archetypes as a whole, individual builds of Shops are weak against individual builds of, say, Big Blue, and this finer-grained relationship between the decks is not captured in the aggregate data.
Fascinating and great posts. There's always: Few people can afford the cost of Workshops. This puts a cap on the number of players who can play the deck, so discourages others from adjusting their decks to beat it, and so it lets the few Workshop players do disproportionately well. What happens if we create a rock-paper-scissors metagame (with the favorable matchups being, say, 60-40) but only let 10% of the people play rock instead of the one-third we’d expect?
That 10% plays rock. 90% play scissors. Rock has a great win percentage, but only because it’s too rare to justify anyone playing paper.
Or, as mentioned, players are not very good at recognizing or switching to the best decks so even if there's a current best deck not everyone switches to it, so it's not worthwhile to build a deck so targeted against it.
An old but relevant post: http://www.archive.themanadrain.com/index.php?topic=21004.msg334559#msg334559
"The price and rarity of Workshops means that Workshop decks are going to be scarce at most sanctioned events (except GenCon and other huge tournaments). This results in Workshop decks not appearing commensurate to their power and makes metagaming against them more difficult."