I have no idea what this kids intentions were. Looks like he disrupted class with an unknown device, an instigation occurred and he was released thereafter.
That being said, when I look at the picture I see a microcontroller, LCD output screen, ac power and battery power. The pencil box is being used to mount the LCD (on the lid) and the microcontroller and battery in the main body. If he added a temperature sensor he could have a device that displays the time and temperature!
You can buy these, and many more, components on the internet for less than $20. Many people such as myself make a hobby out of creating things using these components. I’ve put together simple light/temperature/pressure sensors that record the ambient conditions throughout my house. Everyone of them have displays, circuit boards and wires mounted in off-the-shelf housings like pencil boxes. So if wires and circuits boards look like bombs to you, I would suggest you do not look inside a computer, handheld calculator, your thermostat or any other electronic device. What should scare you is the presence of an EXPLOSIVE substance. I don’t see anything like that in the picture.
Ahmed’s story struck such a nerve because the world saw a model student thrown in handcuffs like a suspect whose crime was being brown.Before we left for the television studio, Ahmed had taken me into his bedroom to show me [Randy R. Potts] the now-famous desk where everything gets built. I asked if I could take a picture; he nodded and sat on his desk chair holding up a tangle of wires, and, seeing his Koran, grabbed it from his desk and held it up next to the wires.
Source: http://www.thedailybeast.com/articles/2015/09/17/man-i-went-viral-my-day-with-ahmed-moahmed-the-most-famous-boy-on-earth.html
That's right, he disrupted the school BIGTIME.
Obviously, it is fun and educational to build circuits, including timer or clock circuits, but a “suitcase clock” is not a thing. I never saw a picture that showed the whole thing well enough to show whether there were suspicious enclosed areas that could theoretically contain an explosive but the consensus from everyone who looked at it was that it did look like a bomb and the theory that this saw unintentional seems like a stretch, especially concerning his behavior and his families political leanings.