No, CTs are not internally shorted. The outputs are externally shorted for safety reasons to ensure the secondary windings are not accidentally open-circuited when current is passing through the primary (as this creates a very dangerous voltage on the secondary). Once the secondary(s) of the CT are connected to the associated current measurement device then the short is removed. If the short was internal inside the CT then the CT secondary current could never be measured.
and then there was the CT that some bloke dropped a wrench on. It became internally shorted! (Caused the motor protection to go south and cost plenty to repair!)
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