Just got off the horn with my cousin, who's sitting at Coronado Naval Air Station, presumably playing Call of Duty or something rather than working. I kid, but still, Navy family comes in handy. I asked him for a final word on the whole "all hands" thing in order to get the record straight.
According to what he was taught in OTC, "all hands" has two meanings. One is official, and is a longstanding part of Navy regulations, dating back to 1843 when the "rules and regulations for the government of the Navy" was first codified. The other is just an offhand jargon term meaning everyone in a specific department, or everyone aboard, depending on who's calling for all hands.
The official, daily one, actually happens twice. Once in the morning at 08:00, with the first call given five minutes prior for all hands to morning quarters, which is the morning formation for muster and inspection, as well as for the raising of the ensign. The second is at sunset, which is another formation for muster and inspection, lowering of the ensign, and release from duty for all sailors not assigned a night watch.
So... it appears that we're all pretty much dead on with assuming that the term, as used, was regarding the morning muster. As for Yorktown calling muster three hours early, sometimes ships acting in active theaters of operation will call muster early, because etiquette takes a back seat to operational need, and she would have been rather occupied with the Philippine-American War going on.