The middle of Linda Greenhouse's latest analysis in the NY Times (which is about the health care mandate case) looks at the strip search opinion(s) and does note that the justices in part 4/IV of the opinion advocated that exceptions may exist:
What's intriguing is Part 4. This section offered an important qualification to the holding. There may be exceptions to the rule, Justice Kennedy said. Keeping a detainee out of the general prison population "may diminish the need to conduct some aspects of the searches at issue." Searches that involve touching – as those at issue in the case did not – may raise "legitimate concerns." There was no need to get more specific, Justice Kennedy said, because "these issues are not implicated on the facts of this case." [I thought they specifically were??]
His opinion was joined in full, including Part 4, by Chief Justice Roberts and Justices Scalia and Alito. Both the chief justice and Justice Alito wrote concurring opinions to "emphasize the limits of today's holding," as Justice Alito put it. "It is important for me that the court does not foreclose the possibility of an exception to the rule it announces," Chief Justice Roberts wrote. Clearly, these two justices were troubled by the implications of the decision, and wanted its limits to be understood.
Among this edgy majority, one voice was missing: that of Justice Clarence Thomas. "Justice Thomas joins all but Part IV of this opinion," a footnote on the first page informs us. But Justice Thomas couldn't be bothered to explain himself, at least not in public. Presumably he shared his thoughts at some point with his colleagues. We're left to infer that what he wanted was a bright-line rule that would admit no exceptions, no circumstance under which a strip search might be so uncalled-for as to violate the Fourth Amendment's prohibition of unreasonable searches.