The actual time that the sun would pass a particular yard would depend greatly on the ship's latitude and heading, as well as the height of her masts, but the phrase seems to have originated in the north Atlantic, where, in summer, this would have typically been at about 11 a.m.. This was the time at which, by custom and rule, the first rum "tot" of the day was issued to officers and men (the officers had their tots neat, while the men had theirs diluted with water), hence its connection with taking one's first alcoholic drink of the day.
The sun is either just over the yardarm or ready to pass under it...no matter.
