Anisa is an agricultural world (not necessarily livestock but probably some). Tami has livestock ranches. Fine Yamataian beef has been mentioned in roleplay, so someplace on Yamatai definitely produces wagyu-like marbled beef. And thus those places produce milk because cows (or generally livestock) make milk. Those planets probably also produce eggs in some quantity.
But this little handful of worlds cannot make enough for the billions of cloned soldiers and citizens. Industrial farming on a planetary scale to make enough for all of Yamatai would have to be even more grimdark than it is in real life.
Instead, I’d imagine that perfectly good milk, eggs, and meat is cloned on a mass scale to meet societal needs. And it’s generally identical in taste to the real thing (because the “omg it’s better than replicators!” thing is such a boring and lame trope). So I tend to think of real animal food products as a super luxury for those who seek it out and can afford it. Which I, as person who enjoys meat greatly and would never give it up but really dislike the process through which humans consume meat, think is completely fine and the most desirable outcome.
On a totally weird note, just last night I was having a (humorous) discussion about the use of Neko milk in Yamataian cooking (misread a recipe page as having “quarter cup breastmilk” and had a laugh). Because there’s that whole thing about how Neko can just produce it on command. It should never be wikified because it’s “ugh no bro” but there is absolutely no way that this abundant milk hasn’t become a regular ingredient for many Neko chefs. You can find real life news articles about speciality ice cream shops selling limited run ice cream that use this stuff from “donations,” so it would probably become completely normal in Yamataian cooking due to every Neko having it on tap for free. Even if it’s spectacularly cringy.