I suspect it wasn't just done out of embarrassment, but also because it could be used for griefing or peole might just accidentally be in a shuttle for an STF. Even if you could still complete, I don't think you manage the optionals. And not getting the optionals has led to some ragequits, I am sure.
Well they revamped the game so that you always have a shuttle and starship ready. Shuttles are for shuttle missions, ships are for... everything else. You no longer need to manually switch to a shuttle to do a shuttle mission. But that does kinda lock you out of doing regular missions in them.
Yeah, why? Player feedback.... related to the debut of Operation Gamma. People hated having to manually switch to a shuttle to do the mission.