Based on your assumptions and what you input for winrates the second time around the conclusion is clear since shops does not have a sub 50% winrate.
I discussed this a bit with Matt and the assumption that winrates are static is what's giving a lopsided equilibrium in this state. Realistically speaking the higher proportion a deck is of the metagame the more people will tune their deck to beat it. This is why we see so many pyroblasts in a metagame where 60%+ of decks are blue. Note that I'm not criticizing what you did: I think it's interesting and it's also unclear how (or minimally a pain) to model tuning decks.
I'm rolling with the assumption that winrates are static for the remainder:
Since as mentioned before the conclusion that shop becomes 100% of the meta appears to depend on none of its winrates being below 50%. You'll notice in your first set of data that shops had a 40% winrate against oath but in the aggregate it had a record of 43-84, or ~51% winrate.
Because of this, a natural question is "how likely is it that shops really has a sub 50% winrate against oath?" The oath versus shops matchup is much discussed, since oath is in many people's eyes the deck to play if you expect a bunch of shops. I do not know much of any stats, but it's fun to learn, so I tried to figure this out. We have a binomial distribution, a sample of n=84 and a winrate of ~51% in the sample size. I had no idea how to figure this out, but based on https://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval the first mentioned method seems reasonably accurate. Assuming I know how to use a z-table and didn't mess up the calculation, it's ~9% likely that shops has a sub 50% winrate against oath, which is lower than I expected. Anyone who actually knows stats should feel free to call me out for doing something stupid