Ok perhaps the disappearance of the Ambassador Class can be linked to Yesterday's Enterprise. A handful were built for testing and deployment and suddenly one, the most FAMOUS one vanishes. Rumors circulate, and intel reveals that the Romulans managed to capture it intact, with living crew-members. It is decided that no further units will be built with that design using that technology-base because the Romulans know every detail and weakness. It is felt this would prove a liability in a conflict.... which never occures because the Romulans withdraw from contact for many years.