“Isn’t someome always manning the periscope?”
No, not always. A boat relies on sonar. If anything or anyone is at fault then it would be the sonarmen on watch at the time. Fishing boats do not make as much noise in the water as larger vessels. With the water being shallow then that distorts sounds in the water because of the sounds bouncing all over the bottom. With all of the sounds in the Strait it would be confusing to a sonarman but a good sonarman should have ‘heard’ it.
A "good" sonarman probably hears every boat in the Persian Gulf--AT THE SAME TIME! As others have pointed out, the Gulf is shallow, and relatively small. Any sounds produced by boats and other vessels radiate and bounce in every direction. And to your statement, fishing boats make just as much noise, depending on their size. Non-military vessels do not put much emphasis on sound-proofing. Furthermore, I couldn't tell from the story where the fishing boat was, if it was moving, or dead in the water. Its first detection may have been only through the periscope. Bad luck, as much as anything else.