So the submariners Stromberg hired were too stupid to realize they were aiming their missiles at a (not so) random stretch of ocean?
Truth in Television: Submarine-launched ICBMs deliberately use a nonstandard and arbitrary coordinate system for the exact purpose of making sure the submariners don't know where the hell the missiles are going. It helps prevent the possibility of, shall we say, submarines going into business for themselves.
If Anya had stolen the plans for the car and knew of its underwater features, why was she so concerned when the car went off the pier? She knew they were in no danger.
She stole the blueprints, but it might have taken her a while to recognise it. They might not have been based on a Lotus Espirit, and besides she might not have thought that the sub part worked (especially if the Soviets tried to copy it and failed), and just believed this was just another James Bond car, as the audience did.