I was in 5th grade, and they didn't tell us what was going on. My teacher just told us to stay away from the windows, and we weren't allowed outside for recess. I remember asking her that if there was someone loose on the playground, wouldn't the younger grades be able to see them? Obviously they couldn't, because there was no one on the playground and we were quite a distance from NYC. I didn't find out what was going on until I got home, and even then I didn't really understand it.
I don't remember if we held a moment of silence the next day, but they would play an elementary school-ified version of "God Bless the USA" over the loudspeaker before we did the pledge, and then we'd carry on through the day as normal. We observed a moment of silence annually once I got into middle and high school, though.