It feels awkward to me to say:
Q : How has she gone to Prague?
A : She has gone to Prague by plane.
Wouldn't this sound more natural?
Q : How did she go to Prague
A : She took a flight.
"How did she go (or, get - as Nate's comment suggested) to Prague?" would sound more natural in AmE. The question could mean a number of things, though:
"By what means did she travel?"
"Where could she get the money for such a trip?"
"How could she leave her infant triplets home alone?"
If you asked the question in the way you propose, it would be with the assumption that the person you're asking had some expectation of the answer you were looking for - i.e., it was part of a longer conversation.