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In Star Trek: Voyager, the Delta Quadrant species called the Vidiians steal organs from all and sundry because they suffer from a degenerative disease called the Phage. Their medical technology is far superior to that of the Federation's and they possess advanced transport capabilities.
So why not just replicate the required organs (since transport and replication are basically the same technology)? Or better yet, clone them (something that even we in the 21st century are close to achieving)?
In-universe, from what we know of the Phage, it is a communicable disease; not easy for other species to catch, but it can spread. That would make cloning organs extremely risky, as extreme care must be taken not to contaminate your source material. The cloning process can also introduce genetic defects; consider taking a piece of paper and making a copy of a copy of a copy etc on a Xerox. Eventually the message is lost completely and you have to start over. With organs, which are perishable, your original organs will be non-viable very quickly and you either have to start cloning clones or simply harvest more organs.
Replication is tricky, and is not quite the same as transport. There are things that can be transported that cannot be replicated; photon torpedoes, for instance, are too complex to be replicated but can be transported from place to place. Replication of foodstuffs is possible, but replication is usually always seen as second-best to the "real thing". If a machine can be sufficiently complex as to prevent replication, and food is never quite right from a replicator, I wouldn't want a donor lung from a replicator.
Out-of-universe, the need to constantly harvest organs of other species makes the Vidiians a particularly frightening enemy faction; while some Vidiians have a conscience and are trying to both cure the Phage and in the short-term find a more acceptable alternative, the majority of Vidiians have rationalized what they do and are all the more horrifying for seeing nothing wrong with it. The Kazon were little more than stand-ins for the Klingons or Cardassians, and as Voyager passed out of that race's home territory their threat diminished. The Vidiians, OTOH, would need a much bigger territory to "farm" for organs, making them a danger for much longer. Once the Borg were introduced as a threat as Voyager entered their home space, the Vidiians also fell by the wayside (the assimilation of an entire person, mind and body, into the collective is just as frightening in its own way as the Vidiians organ-harvesting).
This is just one of the many plot holes and deficiencies of VOY (like how uneducated brutes like the Kazon, who can't even process water, are able to be a space-faring race, much less a threat to species who have mastered basic industrial age technologies).
Given the technological capabilities of the Vidiians, it should have been possible for them to find far more efficient/ethical alternatives to organ piracy:
As far as the threat of replicative fading or infection of replacement organs, these are easily solvable problems with the advanced technology the Vidiians have at their disposal.
Firstly, sequencing the DNA of every Vidiian during the early stages of pregnancy or extracting seed cells from the early zygote would eliminate the problems of copying errors from cloning or genetic damage from the Phage. Individual stemcells can already be extracted without harming the development of the embryo, and it's already common to sequence embryos from in vitro fertilization before one is selected for implantation. One or two seed cells could be grown into thousands, screening out and discarding any cells which contain significant copying errors. Or new cells could be created artificially (via artificial gene synthesis) using the genetic data sequenced during pregnancy.
As far as phage infection, I'm sure the Vidiians are capable of producing clean rooms and employing the same type of contamination control and infection isolation techniques we have today. If needed, all interactions could be facilitated via remotely controlled robots. Or better yet, the Vidiians could simply outsource to or hire other species to man these organ production labs/farms. The Vidiians could then focus all of their economic resources on producing starships, weapons, or other manufacturing, and trade these goods or their medical services with other species for fresh organs.
So why do the Vidiians resort to organ piracy? Well, the only logical explanation for that is that their society has outlawed all of these more ethical alternatives, and black market organ harvesting arose to meet the demand. Though even this explanation is pretty thin...
The Doctor had asked B'ellana Torres to donate her tissue sample to Denara Pel, and successfully started genetic cell regrowth. There is your guinea pig.
I guess because cloned organs are already familiar to the phage virus and they will perish quickly, so they need new organs the phage virus isn't familiar with.
