So it’s made of shit, right? And shit is an animal product. But barring a night of drinking or a particularly aggressive burrito, shitting does not harm the shitter; it’s beneficial and required. Also the animals in question can and do consent, does that make it vegan?
The problem with hardline dietary veganism is that if extended to its logical conclusion, molecules are just molecules and they’re all by definition interchangeable with each other with no way to distinguish them. It’s unlikely that any vegan foodstuff does not contain a single molecule that was once part of an animal, no matter how distant or how long ago, and quite impossible to actually verify if this is or is not the case. I’d doubt there is much water on Earth by now that hasn’t been peed out by some animal at least once, be it a mammal, fish, dinosaur, trilobite, anemone, or prehistoric crypid deep sea monster.
Ultimately you have to draw a line somewhere, and in the case of Trek replicators it’s pretty clear that once matter is broken back down into its atomic or molecular form to be reassembled in the later replicator it is in no way related to what it used to be. And remember that not just human waste is used as feedstock for the replicators anyway; raw materials are also used.
The interchangability of atoms isn’t the concern, but whether the food contains the animal proteins or other substances which a dietary vegan is avoiding for whatever reason.
I mean, proteins are complex structures made up of atoms, so rearranging them into a different structure would make them no longer a protein molecule, animal or otherwise…