An interesting precedent to what I suppose will now be the Hussein Case seems to have occurred in the British intervention in Sierra Leone in 2000. It might well throw some light on the differing views of legality and its importance between the UK and US to consider what happened immediately after the capture of the RUF leader Foday Sankoh. Sankoh - whose movement famously engaged in mass amputations of prisoners' limbs as a form of revolutionary terror - was taken prisoner at a house in Freetown very soon after the British force landed. The initial problem was to prevent his followers from springing him, not to mention preventing a lynching. The obvious solution was to load him into a helicopter and ferry him without further ado to Illustrious, the task force flagship. But there was a serious difficulty in using her as a jail, which was that according to the law of the sea, she was under exclusive UK jurisdiction. That meant that he could legally claim refugee status immediately his feet touched the deck. In the end he was held in the Freetown prison awaiting trial by a UN-supervised court set up after the RUF's defeat later that year (he died in prison).
The Americans, though, occasionally give the impression that third-country prisoners are being held aboard ship. Whilst those ships are on the high seas or in US territorial waters, they are technically part of the US courts' jurisdiction for any event aboard. In foreign waters, the principle is the same - but with the condition that the port state has jurisdiction on any matter affecting its peace or security. Either way, they are either not holding prisoners at sea or they simply find the law inconvienient.