Can a ghost throw an EMP while sitting inside a bunker?
No, you cannot use special abilities of units garrisoned inside a bunker, with the exception of stim packs. It's not even possible to individually- or group- select the units inside, though you can direct their fire by right-clicking.
I've just checked and stim is unique in that it can be activated on all units inside the bunker (as long as there's at least one unit inside capable of stimming).
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