In my experience, they sweep the coin lockers when the station closes down at night. If you lock up a bag overnight, you will have to pay the cost of the locker again to get your luggage back. (This happened to me at Keisei Ueno about 2 years ago when I spent the night out before a morning flight from NRT.)

Takkyubin may be a better idea in this case, since they're going to charge you for the extra locker time in any event. I don't know if they'll destroy your bags, though.