I seem to recall that Deep Space 9 touched in this in various ways during its run. Keep in mind that it was the first series that was fully made without Roddenberry input.
TNG, Voyager and Deep Space 9 all at various points made an issue of how the replicated food was not quite the same, without really trying to explain why (a lot of the issues with our mass produced food is exactly that: it's been modified to suit mass production, transport and storage, and often to be cost reduced as well; you'd expect most of those issues to disappear once you're using a replicator).
But you're probably right that DS9 made a bigger deal of it, especially with Sisko's dad and his restaurant featuring more than once, as well as various luxury products fetching high prices, when you might otherwise assume such high prices would quickly ensure they'd get replicated.
> TNG, Voyager and Deep Space 9 all at various points made an issue of how the replicated food was not quite the same, without really trying to explain why
I believe there's a good hint when you combine some stuff from across TNG/DS9/VOY: Replicator patterns are relatively low-resolution for storage.
They only go to the molecular level, not the subatomic/quantum level [0], and even then occasionally have issues [1]. And even if you had a high-quality pattern stored, the replicators themselves are built around that low quality, hence why the genitronic replicator was needed for Worf's spine [2].
Transporters are built on the same technology, but work at the much higher resolution necessary to break down/rebuild a person. However, the amount of memory needed for that is insane [3], hence the specially-designed pattern buffers, which under normal circumstances degrade very quickly [4].
TNG touched on it I think - Deanna once tried to have the computer replicate her a chocolate sundae or some such, and it was implied if not outright said that the normal sundae was modified to be more nutritious. I’d imagine tweaking the “junk” out of desserts would make them taste different even if you have molecular control over the results.
You'd think that LaForge, or at least Crusher the younger, could do a hoppin' side-business with just one replicator hacked to bypass the nanny functions that turn alcohol into synthahol and chocolate into cocoa-flavored nutriment.
I saw that in the new Lost in Space series, where the 3D printer refused to print a firearm in an emergency, and thought to myself, "ohhhh no you di'n't!" In my mind, I was already patching out the DRM function, or adding stray non-functional voxels to fool its pattern-matching.
That was one of the things I disliked most about TNG, where humanity intentionally crippled itself by installing nannybots everywhere. DS9 brought some of the dirty reality back, with Ferengi-run gambling and holo-prostitution and cops that were actually people. Or goo pretending to be a person, anyway.
