I always just assumed it was an innate ability of the owls; if they were being followed, they wouldn’t deliver until the coast was clear. Kind of like secure mail.
I don’t know much about the prefect system, but don’t you have to be a prefect to be made Head Boy? In the first book, Hagrid tells Harry that his parents were head boy and girl when they were at school. But in OotP, Sirius mentions that Lupin was made prefect because he and James got into so much trouble. So how does that work?
The best explanation I’ve seen for that one is that Hagrid doesn’t have the most reliable memory. He liked Harry’s parents, he thought of them as a couple, he maybe thought that James should have been Head Boy, and maybe Lily actually was Head Girl. It’s easy to go from remembering “Lily was Head Girl, and Lily and James were a couple” to instead remembering “James and Lily were Head Boy and Girl”.
Especially since James was a Seeker, which put him on par with the Prefects (just like Harry with his mates).
I thought Harry got access to the Prefect’s bathroom (which was one hell of a bathroom!) because he was Captain of the Quidditch team. He’s been Seeker since his first year. I’d assume James was Captain of his team as well.
And you know, even if there was no way to locate Sirius via GPS’d owls, you’d think his enemies would have at least tried to harass him that way, by sending him a Screamer every hour on the hour.