My profile on Thingiverse declares that I'm a "tinkerer". Of the options they had, that one's pretty close to right. I like to build stuff and modify things. As kid I tried to build a robot hand and as an adult I've built several robots. When I was young I had to salvage motors and gearboxes from toys and appliances, while now I can order inexpensive(-ish) mechanical and electronic components designed for hobbyists off the internet. Ahmed Mohamed is also quite familiar with hobby electronics, and the clock he made looks exactly like a hobby electronics project.
A one-off electronics project will typically consist of four things: a microcontroller, input & output devices, a power supply, and a case. That's all clearly present in this design. The central circuit board is some type of microcontroller. This is wired to a 4 digit LED display and another board that's not clearly shown but probably contains a speaker (since the story mentions that the clock "beeped"). Those are the outputs. It's clearly using a transformer for power, but there's a 9 volt battery connection as well for remote operation. The wiring is a mess but that's also typical. These kinds of things are cobbled together with whatever bits of wire one has on one's work bench. Because it's messy you usually put it in a case (called a "project box") to hide all the stuff you don't want to see. But Ahmed didn't want to hide his work -- he wanted to show it off. That was the whole point of the exercise for him. Since he couldn't just carry around a wad of electronics, he mounted it all inside a case he could open.
So to my eye the design all makes sense. It looks like any typical hobbyist electronics project. While it's clearly not a bomb (there's no explosive), part of it indeed looks kind of like a bomb might look. A home-made bomb could look very like any home-made electronics project: microcontroller, power supply, inputs & outputs, one of which would be the trigger for the explosive charge.
However, despite the fact that it looks like part of what a bomb might really look like, the questioning, arrest, and suspension of Ahmed was unjustified and racially motivated. The school officials and police consciously or unconsciously expected that if there was terrorism it would come from middle-eastern looking people. So when a dark-skinned nerd has a project that looks bomb-ish, he gets charged with making a fake bomb to scare people, a charge that's effectively terrorism. There are plenty of white people with sinister intentions and more means to carry them out that could be called terrorist, but aren't.
People may still say that he should have known that people would think his clock was a bomb, and made it look less threatening. Not only is that victim blaming, it completely fails to understand how 14 year-old boys work. There's a reason why it looked to officials like a Hollywood bomb. He didn't just want to make something functional, he wanted to make it look cool. And stuff from Hollywood action movies is cool. A nerd opens his nondescript case and there's some hacked-together electronics and a digital readout ticking over? That's cool. It looks just like the kind of device that James Cameron might put in the hands of a white protagonist. What kind of nerd creates his own spy gear? A super cool one.
Ahmed -- it's a good bet -- is a fan of action movies, if only in a small way. Fans of a thing want to create more of that thing in their own lives. It's why fans dress up in costumes, write fan fiction, collect toys and replicas. That's why Ahmed would want his project to look cool in an action-movie way. If you can create something more of what you love, why not?
The problem is that fandom is racist (and sexist). If you're white and male you can find plenty of role models; if you're dark-skinned or female, not so much. Because the media shows us so few dark faces or women we assume people like that aren't fans. At least not true fans. So when we as a culture see a middle-eastern child playing with some electronics we assume it's a bomb and he's a terrorist. When we see a black child playing with a toy gun -- because guns are also cool in action movies -- we assume it's a real gun and he's a gangster. And we put him in jail, or gun him down in cold blood.
The victim-blaming has to stop. Kids must be allowed to be kids, and oddly enough we can contribute just by letting everyone express their fandom, and giving everyone heroes that look like them.