There are tons of traditions, this is one.
Some make sense, some not. A lot of Mids like to push boundaries. I know on the outside it seems like why would someone break the rules? Because Mids are still mostly 18-24 year old college kids who like to have fun. Alcohol and fun does not always equal good decisions. Also, you will realize that good Mids can make some bad choices sometimes. The reason it's done at night mostly is because that is when all Mids are around, generally company officers and senior enlisted are around and its when things sort of wind down for the day. Also when I was there if a Mid did something Bad enough to get that many demerits and be retained it was a huge relief. That is an extremely stressful time for them and you never want to see a close friend go. Off the top of my head I had the following friends get Black Ns: one is now a Marine LtCol and F/A18 pilot, another was a Brigade Commander first semester and got one second semester, one is an astronaut, another is a permanent military instructor at USNA, another was just selected to be a Commanding Officer in the Navy, another has a PhD and is a Navy SES. As you can clearly see stupid conduct offenses does not mean bad Mids or humans. It means a bad moment in judgment, many times its alcohol fueled and others its Mids pushing boundaries with a work hard play hard mentality of a young adult blowing off steam. It's a matter of their character, potential and performance that keeps them there.