I don’t know if the Wish Gem could be targetted. But what I do know is the Bomb Gem that can only be activated by being destroyed or exploded. Can’t be targetted by a destroy gems troop. 
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Wish gems also could not be targeted.
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So, despite being named “gem”, they have never been consider gem at all.
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What else did you expect, really?
Clockwork Sphynx destroys gems of a chosen color and bomb gems are of color…well, they don’t have one.
Anything that destroys random gems works just fine.
EDIT. What is sad, though, is that it can’t be targeted by explode one unspecified gem troops (like Ancient Golem and such).
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That spell was written years before things like Wish Gems and Bomb Gems were a thing. So EVERY gem had an actual color.
I do not for see the devs going back and rewriting troops spells. But it would be nice if the actual intention of the cast could be met.
As you mentioned in your post. Even gems without a color handicap can’t target a Bomb Gem. So I don’t think color is more than just a way to describe the cast rather than an absolute rule.