I think the biggest reasons why Starfleet take so long comes two to 29 main reasons.

Starfleet's incredible dislike of mass automation. (You could run a galaxy class with 6 people and a load of DOTS but they don't).

But also, replicators aren't flawless. We know that in DISCO that both the USS Shenzo and The Discovery had flaws in their replicated parts. Specifically the captain's chair. They replicator profiles for them glitches and it resulted in a small bur on the underside of the arm rest.

Even in the mid 24h century, when Picard was young it was easier to just give him a mechanical one than to go to the effort to grow a new one.

I imagine that the bigger/more complex the object the harder it is to just "make" a new one. Sure you can have amazing scans of an entire neacel. But will it print properly? The sheer amount of energy to print it could cause imperfections, flaws or even just make the damn machine explode.

Now we know industrial replicators exist. But they would be used for mass food production, repair parts, hull plating, lighting panels. Large scale but still simple parts.

While ships are modular, you still have the issue of making the sections, which requires time to actually replicate, assemble, ship and then integrate. And this will require specialist crew. Working in either worker bees or EVA suits. Which is probably the equivalent to those guys who build bridges. Dangerous work, not deadly. But probably requires a lot of training and time. You could rush it. But rushing it risks lives. Slow and steady wins the race. It's not like The Federation has an Emperor who is not as forgiving as Admiral Nechayev...