As in, high school students don't have the same free speech rights as adults, but they don't lack them entirely.

You may find the wikipedia article on Morse v. Frederick (aka the "Bong Hits for Jesus" case) interesting reading.

While I haven't read the recent TX judgement, I think the short answer is probably that speech promoting drugs is harmful, speech promoting sexual promiscuity is harmful, but speech promoting a religion is not harmful. Therefore the latter is allowed under students' limited free speech rights where the former two are not.