The Jack that you're referring to (48 stars on the blue field) is only flown by the USN in port, from the jack staff on the bow of the ship in combination with the National ensign being flown from the stern. As soon as the ship is underway and no longer mored to the pier, that flag goes bye-bye and the National ensign is raised from the yardarm on the main mast of the ship. The stars and stripes are always present, even underway, so changing the USN flag to that wouldn't make too much sense, unless TNF/SDE forced all players with USN ships to never leave the harbour ;-)
EDIT: Also, it's important to note that unlike most naval powers at the time, the USN is one of the few that does not have a separate unique flag that they fly instead of their national ensign. For instance, British warships in WWII didn't fly the Union Jack, they flew the white field with red cross over it, that had the Union Jack in the top corner at the hoist. The Kriegsmarine was the same, and had possibly one of the more beautiful naval flags in WWI (white field with a black cross, imperial eagle, and then the German Military's flag in the top corner on the hoist, look it up sometime).
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