Re. the OP, Memory Alpha just says latinum "cannot be replicated," and it doesn't explain why. I think I've read a little bit more complete explanation in one of the novels...but I can't remember anything about it. I'm thinking this might have been in Hollow Men, since I read that fairly recently...does anybody remember better than I do?
As for the general idea that replicators create perfect replicas of everything...you know, I just don't think so.
I'm a cook - not professional or anything, but it's one of my favorite things to do, and I do it a lot. From scratch, mostly, and mostly with fresh ingredients although there are exceptions to this since there are times when canned or frozen ingredients are greatly superior to, for example, those tomatoes imported from Alpha Centauri or wherever it is (some place where tomatoes are supposed to be orangish and waxy and dry and mealy and utterly flavorless) that we get around here in January.
A lot of people don't cook this way any more, and I can understand why - almost everybody is short on time, everybody has to allocate his or her time in the best possible way, and if you don't have the time to spend in the kitchen or you'd rather not spend your spare time that way, so be it.
But do you know - and you other dedicated cooks out there can attest to this - how often I'm told some piece of over-processed and/or mass-produced and/or artificially flavored dreck is "just as good" as homemade or "just as good" as fresh or "just as good" as the real thing? All the time, that's how often. Is it ever true? Sometimes. But most of the time? Definitely not.
Is artificial vanilla as good as real vanilla? No. Is frozen sweet corn as good as sweet corn that was picked just a few hours before? No. Is non-fat ranch dressing as good as real ranch dressing? No.
Just last week, an in-law was talking about how much she loves these pre-packaged apple slices. The processors take fresh apples, core them, slice them and treat them with citric acid or something so they don't turn brown, and this in-law just loves them and eats them all the time.
"So what's wrong with just eating an apple?" I wondered to myself. I mean, apples are in season right now. They are cheap. They are available. There are orchards and farmers markets all around the city where you can get fabulous apples practically or literally right off the tree. I have Ida Reds and Jonagolds from a local orchard sitting in my kitchen right now. And yet she's paying an enormous premium for apples that have been sliced and treated, and she's doing so right now, while apples are in season.
I guess if it keeps her from eating potato chips, that's something, and I could understand it if she explained it that way. But that's not the deal. No: she actually thinks those silly apple slices are as good as - are better than - an apple that was picked off a tree just few miles away just a few days before.
She can't taste the difference. Or really, I guess she can, but she prefers the taste of the processed product to that of the fresh, local product.
My point, which I realize I'm making in a circuitous way, is that although I'm sure the Trek replicators can do a perfect job on some things, a great job on other things, and good job at some things - they'd pretty much have to do a better job with tomatoes that whoever grows them on Alpha Centauri - based on my experience as a cook, I am also pretty sure that some things just won't taste right. And some of them won't taste right because they aren't right - they are close to the real thing, but not...quite...there.