I don't have it on hand but in a Star Trek Online Starships Collection magazine, the strange nacelles of the Age of the Discovery were explained due to Starfleet trying a brand-new warp drive instead of the "Cochrane-Archer" drive, the "Kurztman-Beyer" drive. During the Klingon War, Starfleet was decimated. Finally, in 2259, a shipyard with many such ships was abandoned due to a stellar event, prompting Starfleet to abandon the Beyer drive in favor of the Cochrane drive, ergo focusing on round nacelles again.