As a counterpoint, since we're all just dealing in anecdotes here, I had a non-empty answer to the "Discipline Question"; I was suspended for "hacking", albeit after voluntarily telling my principal about it.
I disclosed it on my applications, while my high school did not. I was still accepted to MIT and Stanford. I later learned that MIT actually called my high school to get clarification on it, so I know it was seen at least by them.
I was also a finalist for an NSA scholarship program (flown out to the Maryland "friendship annex" for interviewing) despite having disclosed it.
So, I dunno what my point is. Maybe these things depend on who reads your application or what, but it's not an automatic dealbreaker, and I do encourage people to be honest.