They could just make it so "Pokémon with Wonder Guard cannot Terastallize"
I can see them doing three things:
1. Wonder Guard simply turns off when the user Terastallizes.
2. Wonder Guard makes it so only the users original weaknesses cause it damage.
Now the above 2 kind of makes Terastallizing a Wonder Guard Pokemon pointless. BUT then there's:
3. If a Pokemon with Wonder Guard Terastallizes into a Type it wasn't originally, it'll actually be treated as if it was its original Type(s) and the Tera Type.
So, in Shedinja's case, while there would be no change to what could hit it if it was Tera Bug or Tera Ghost, for the other Types only the following could hit it:
Bug/Ghost (5): Flying, Rock, Ghost, Fire, & Dark
+Normal (4): Flying, Rock, Fire, & Dark (loses Ghost)
+Fighting (5): Flying, Ghost, Fire, Psychic & Fairy (loses Rock & Dark)
+Flying (7): Flying, Rock, Ghost, Fire, Dark, Electric & Ice
+Poison (6): Flying, Rock, Ghost, Fire, Dark & Psychic
+Ground (6): Flying, Ghost, Fire, Dark, Water & Ice (loses Rock)
+Rock (5): Rock, Ghost, Dark, Water & Steel (loses Flying & Fire)
+Steel (3): Ghost, Fire, Dark (loses Flying & Rock)
+Fire (5): Flying, Rock, Ghost, Dark & Water (loses Fire)
+Water (6): Flying, Rock, Ghost, Fire, Dark & Electric
+Grass (6): Flying, Rock, Ghost, Fire, Dark & Ice
+Electric (4): Rock, Ghost, Fire, Dark (loses Flying)
+Psychic (5): Flying, Rock, Ghost, Fire, Dark
+Ice (6): Flying, Rock, Ghost, Fire, Dark & Steel
+Dragon (7): Flying, Rock, Ghost, Dark, Ice, Dragon & Fairy (loses Fire)
+Dark (4): Flying, Rock, Fire & Fairy (loses Ghost & Dark)
+Fairy (5): Flying, Rock, Ghost, Fire & Steel (loses Dark)
So, if I did that all right, we create quite the interesting list of options.
* Not surprisingly, Steel is the best knocking it down to just 3 of its original weaknesses with Fire and maybe Dark being the most threatening thing to it. PLUS Steel gives it immunity to Sandstorm and Poisoning.
* Normal, Electric & Dark knocks it down to 4. Normal and Electric simply removes one weakness while Dark takes two but adds one of its own. Of the three I'd say Electric is the best as it not only takes away but also gives immunity to Paralysis. I'd argue Dark is probably the worst as, while it changes the Types up a bit more, it adds Fairy which is more common. Normal's loss of Ghost is nice but it's an uncommon Type so situationally nice.
* Fighting, Rock, Fire & Fairy makes things interesting by having the same amount of weaknesses, though it's not always beneficial. Fairy swaps one for one, though it's for the somewhat common Dark for the least common Steel, making it the best here. Rock also adds Steel, but also the common Water, but removing Fire and Flying makes it comes out about equal I say. Fire less so, think Water immunity is more wanted than Fire, even with the added Burn immunity. And then there's Fighting, ugh, gaining Psychic & Fairy for Rock & Dark was not a good exchange; maybe good for the initial trip up, but afterwards makes it feel more vulnerable.
* Psychic offers no changes, lol.
* I commend Ground for trying, but not only is one-for-two still not good it's also of more common Types.
* Poison, Water, Grass & Ice offer nothing but more trouble; I guess at least Poison offers immunity to Poisoning and Grass to Powder & Spore Moves...
* Dragon... I'd say I'd also commend Dragon for trying, but did it? Like is the loss of Fire really throwing anyone for a loop, especially when it now has weakness to common Fairy and Ice? This is one case where adding Dragon isn't helpful.
* Go home Flying.