Star Trek's theme is that natural is preferred whenever possible
Oh? To the contrary, whenever somebody tries to go natural, Starfleet sends in Kirk, who blasts the organic paradise to bits with infrasounds and then deports the hippies!
Also, synthetic Lieutenant Commanders apparently are to be preferred to organic ones.
"Natural" never held much sway in Trek, except in the broad sense of "natural order of things" which generally was defined by industrial rather than pre- or post-industrial standards...
Apparently, manufacturing replicators ain't so simple.
Which is weird in itself. Make one and you have a billion!
Apparently, there are replicators and then there are replicators, though. The shipment of "industrial" ones to Bajor in "For the Cause" might have kickstarted a replicator-based economy on the planet, if not for the theft. One of
those babies could have provided every home with a food replicator, assuming enough power was available. And Bajorans did seem to be thinking that power is food back in "Progress" already, where they destroyed an entire planet (well, moon, by somebody's definition, but those are fuzzy) full of life and food in order to get power.
Soil reclamation as in "Shakaar" I can understand: replicators would supposedly make these people more dependent on the central government and its infrastructure, while farming might sustain them independently of the state. But replicators would feed them better and more securely.
Hunting for pleasure is probably outlawed or looked down upon.
To the contrary, both Sisko and Riker are known to fish, with no social stigma attached. Apparently, giving the victims a fair chance is fine, while enslaving in raising pens and the like is not.
Then again, we only saw Sisko holo-fish. If the unreality of the situation makes it dandy, then eating raw flesh including the still pulsating heart of the poor beast ought to be fine, too, provided this flesh is replicated.
As observed, Sisko father serves real shell fish
All we know is that he serves things that need to be processed first, the way real shellfish would. But he thinks that cooking that way is fun - so for all we know, he gets synthetic shellfish that he then prepares the traditional way.
We've seen "home cooking" in TNG and DS9, labeled as highly exotic and eccentric. But we haven't seen where the ingredients came from. Hardly from the local arboretum, I'd think. More probably from the replicator!
Timo Saloniemi