I think that the school did the right thing. Homemade digital clocks have been around for fifty years. You can purchase a kit for under $10. There is nothing special or unusual about a kid assembling a kit to make a digital clock.
What was unusual was to package the "clock" like a bomb. That appears to be deliberate.
You can get digital clocks in many colors, sizes, and shapes that do not look like a bomb.
Where is the journalism in this? Was he working on a science project? Or was he bringing in something for show and tell?
He probably saw one that his Father had made and copied the design.