Stripped naked and search is standard custody practice. Criminals hide things and are known to smuggle things in and out of court to prison. And remember, he is techincally a criminal. He broke criminal law when he skipped bail. He is being held in custody, it seems fair for standard policies to apply to him. Why would he be any different?
It is standard for someone to sit in the dock, why would he deserve special treatment. He is able to confer with his lawyers when he needs to from the dock as many other people have done so in the past and will do so in the future.
The only issue I have is them taking his case files, which seems petty. But I suspect there would have been operational reasons, but why those reasons couldn't have been worked around seems odd and again petty.
While I think he doesn't deserve to be sent to the US and should not be. The fact, he is a criminal and is in custody because he can't be trusted does mean he should be treated as such a manner.