I work, and have worked for 29 years, at Norfolk Naval Shipyard. Prior to that, I served in the US Navy for six years. I would bet that I have seen a few more ships and shipyards than you have. You should know, seeing as your son is a junior officer, that the taking of photographs in a naval shipyard will get you promptly arrested and charged with espionage unless you have a special permit and special permission.
When a ship enters the Yard, cleanliness is soon lost in the grime, grit, dust and smoke of the business at hand. The ship's force and shipyard work force do their best to keep the ships free of debris. But, since the ship is going to be repainted before it leaves anyway, the condition of the hull and superstructure are of minor importance.
edit: Since San Diego was mentioned as a place where a shipyard was, I am taking this as a mistaken identification between a shipyard and a naval station as there are no naval shipyards in San Diego. If you are referring to a naval base, then i can agree with you.