I used to be firmly in the Energy Flux camp on this one. (I still think Flux is just crushing, and at least in Control Oath, which runs a bit mana dense, it's pretty good. They can make all the thopter tokens they like.) However, watching Rich Shay, and also my wife as they run Xerox, the 1for1 cheap removal game is viable at least. Shattering Spree is probably the best in that vein, since it can be, but isn't limited to being a 1for1. As a passive observer, it does seem that blunting, and finally taking apart their board with spot removal is viable.
@Griselbrother how is 3 mana prohibitive! I'm confused. Are people saying that any deck other than Shops has an impossible time generating enough mana to play 3-drops on turn 1 or 2? I think in the past week I've had 2 people drop Jace on turn 1 against me while I was holding a t1 3-drop. If you drop a Prison t1 or even t2 against Shops, They'll most likely have to make a decision of whether to attack or cast spells which can buy you time, and they can't pay for Prison with Shop mana. It's not the greatest thing in the world, but in combination with Null Rod, Suppression Field, targeted removal, etc, it can do work.
3 mana isn't impossible to get to, yet it's still worth mentioning that Hatebears has a harder time getting to 3 mana than most other decks because of the lack of draw and card filtering.
I think the problem is that people want a "Golden Gun" against any deck, like they want to bring in one card from the SB without thinking too hard and just draw it and then their opponent scoops. I can think of several combinations of the cards mentioned that, together, could incapacitate a Shops deck, and many others. Since they're incapable of running crippling taxing effects now and have basically stopped putting things like Tangle Wire into the deck, having 2 or even 3 cards that are really good against shops (but not golden gun good) is perfectly reasonable. I don't think they'll print this for us:
Magus of "I Kill Shops Decks"
Flash, Haste, Hexproof.
T: Destroy all artifacts your opponents control.
so... We might as well just pick things that have the broadest applications in Vintage and use a few of them. Personally, I have 3 Kataki, 3 Stony, 2 Muse, 3 Relic Warder and more, and I'm trying Suppression Field in the SB, but I'm not personally sure it fits into my deck yet. One thing I am quite sure about is that Ensnaring Bridge isn't going to work unless the deck is built around it, and with JUST Bridge and your hand at zero cards, I'm not even sure it would be effective when Ballista is a card.
I agree with your statement that you, in general, want to play cards that have a broad application, which I believe I also mentioned earlier. I also wrote that "In my experience it takes a pretty dedicated build and a combination of quite a few cards to beat shops" which pretty clearly indicates that I'm not looking for a "Golden Gun" against Shops. While I do think that Ghostly Prison has some application across matchups (although it's definitely not what I want to be doing against Delver/Pyro/BUG), I think that it's actually an example of such a "Golden Gun" and probably not a very good one (though it should be said that I haven't tested it) because it's a) slow and b) can be played around.