Didn't the clock boy basically just pull out a clock and put the insides in a different container. Plus he got in trouble for when he pulled it out or when the alarm went off, the reaction assuming it may have been a bomb was like all stories about schools reacting to kids and anything vaguely resembling a weapon, over blown.

besides a fake small bomb is easier to believe would be brought to a school for something terrible, than someone actually making and bringing an atomic bomb to school.