I recognize that he didn't have a warrant out for him, but from the cops highly mistaken point of view, he did and that's what matters here.
From the jailer's point of view, you can't say that there's no reason to suspect he had something on him. They're going to assume that everybody does. As for the second jail, yeah, it seems pretty silly. Here's something to consider, though. In matters of law enforcement, administrations often take a zero exception approach. There was a story down here a few years ago about a little old lady in Highland Park (the richest neighborhood in Dallas). This woman was 90+ and didn't have her license on her. The policy of the HPPD is to arrest people who are driving without a license, and she was no exception. They cuffed her and hauled her bony ass to jail. They caught a whole bunch of flack for it, and their explanation was that if they cut a break for her, then they'd catch flack from everybody else that didn't get one. Since they deal with filthy stinking rich people constantly, and they have a keen interest in avoiding the appearance of treating them better, they treat them the exact same way they do the Mexican maids and landscapers they pull over. On top of that is the bureaucracy involved in running a jail. Hell, they actually lose prisoners sometimes. Rather than determining who's searched and who isn't searched when transferring in, they probably prefer to search everybody. How do they know if #24601 came from city A that routinely searches people, or your preferred city B where they don't? I can see how they might have searched him at the second jail and it wasn't because they wanted to fuck with him.
And that's not a legal basis for awarding somebody damages. I'm wondering what hook the courts could have hung their hat on in determining that you can't strip search people lawfully detained?