The difficulty with the decision is that an opposite decision by the Court could have been interpreted as prohibiting strip searches in cases where they are appropriate.
The decision doesn't say that every prisoner must be stripped searched. It only allows the method where the detention authorities think it's needed.
A frequently ignored principle in evaluating court decisions, especially for SCOTUS, is that the Court is only allowed to consider questions posed in the complaint, and apparently the petitioners didn't complain about idiots and perverts being allowed to work in detention facilities, so the Court couldn't say "don't do that."
Essentially what the Court said was that it's up to those who make the laws in each jurisdiction to decide when such things are prohibited, and unfortunately that's left to someone else in the system. The Court can only decide whether the laws that exist are permissible according to higher laws, and in the case at hand it's fairly obvious that many lower jurisdictions haven't considered it important to regulate which prisoners are treated in what ways.