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.
A nice theory, but there are two problems with it (or at least one problem that's canon):
a. The disappearance of the Ent-C was a complete mystery until Picard met Sela. So even though we the audience knew what happened, Starfleet didn't, so there wouldn't have been any intel about the Romulan involvement. The last official Starfleet/Romulan contact was the Tomed Incident of 2311, so no one knew about what happened at Narendra III.
b. According to my timeline (which of course is conjectural based on registry numbers), the Ent-C was destroyed 30 years after the Ambassador class was commissioned. So Starfleet had thirty years in which to build a ton of Ambassadors before the Ent-C met her fate, so the Romulans wouldn't have been the reason why this didn't happen.
Also, if Starfleet did have intel that the Ent-C was captured intact with a living crew, at the least there would have been a rescue mission to retrieve the survivors and the ship, and at the most, the Federation would have declared war against the Romulans. Neither of those things happened.