Mirandas were in use during the Dominion war but I think they would have been retired by 2409. I agree with this poster that if these ships were not in game players would want to have them anyways. The timeships are still rare enough that if you dont like them you can ignore them. I think the Miranda and constitution should have been lockbox or c store ships to make them uncommon too. Although you captain a ship at ensign rank so an outdated miranda makes some sense for a first ship, but a shuttle may have been a better first ship..
They didn't replace the Mirandas with anything else and they needed general workhorse ships. IT could have been Nebula but the Galaxy era were too gigantic and bulky to reproduce efficiently at the time.
The way I see it for these special circumstance ships is that they're replicas to study. Excelsiors and Constitutions were refitted and retrofitted to death and beyond as Starfleet doesn't like throwing away ships when they need them. No doubt Kirk had something to do with that.
The real issue is that Cryptic treats lore as an afterthought instead of making things known.
Mirandas do have a replacement, the Shi'Kahrs. However, that is one of Cryptic's failings, They add new stuff without really explaining it or adding a backstory to it. Yeah, they give us dev blogs, but they really don't say too much.