There's an "FAA technical problem" in keeping a "baddy" in manacles during critical phases of flight, I believe, in the interests of his/her safety.
Also, certain countries where booze is not permitted will sometimes deport "booze" offenders and I have heard of these being escorted to the airport in manacles and handed over to the flight. Not sure at what stage the 'cuffs" come off, but I'm sure the authorities do not let the manacles go with the flight!
Of course, in these cases there's no need for the cops to meet the deportee at his destination!