I originally thought Shadow Stitch goes through Magearna EX, but after comparing some text, Shadow Stitch should definitely be blocked by Magearna EX.
Until the end of your opponent's next turn, each Pokémon your opponent has in play, in his or her hand, and in his or her discard pile has no Abilities. (This includes cards that come into play on that turn.)
To me, the focus here is that it specifies the cards and not the player.
Now let's look at other cards that we know are blocked by Magearna EX
Plea GX
Put 2 of your opponent's Benched Pokémon and all cards attached to them into your opponent's hand.
We know for fact that this targets the Pokemon. Stating "your opponent's" is simply a range of effect declaration, meaning that the player activating Plea GX can't use it to the same effect as Acerola on themselves, which could actually be very useful.
Here is Miraculous Shine
Devolve each of your opponent's evolved Pokémon and put the highest Stage Evolution card on it into your opponent's hand.
Once again, stating "your opponent's" is only a range of effect declaration so that the player using Espeon EX's attack cannot devolve their own Pokemon, for example devolving a Gallade to turn it into a Gardevoir GX next turn.
Shadow Stitching, Plea GX, and Miraculous Shine either all are affected by Magearna EX, or none of them are affected by Magearna EX.
This is Sparkling Wish, which is not affected by Magearna EX
Search your deck for a card that evolves from 1 of your Pokémon and put it onto that Pokémon to evolve it. Then, shuffle your deck.
This attack is a command for the player using it to take a particular action and does not influence any Pokemon on Magearna EX's side of the field. Thus, it's okay and Magearna EX does nothing.
So here's the bottom line:
As long as the active Pokemon receiving the attack has a steel energy attached, it negates attacks such as Shadow Stitching, Plea GX, and Miraculous Shrine before they can even spread to the bench.
Basically, what PMJ said in the first response.