I'd like to propose an alternative crack theory to the crack theory that Anya is royalty.
The dead empire has been dead for a long time, possibly hundreds of years. The only part of it that seems to still persist is Garden. Shopkeeper even controls and lives in the royal palace, suggesting he may be descended royalty himself. Loid is surprised that Anya is good at the ancient language since almost nobody speaks it anymore, but if anybody is going to speak it, it's going to be Shopkeeper. Possibly some of those around him too.
During this arc, we were introduced to three new pruners: Hemlock, Gympie, and Thistle. Thistle doesn't appear. Maybe he or she just wasn't relevant, but then again, Gympie was hardly relevant and she still showed up. I have nothing to substantiate this: Axeman made sure to name drop Thistle because it's important that we know she exists, but he chose not to show her because we've already seen her and her appearance is a massive spoiler.
Thistle is Anya's mother. Anya is good at classical language because she was born around the final vestige of the empire that natively spoke it.
Things that could figure in somewhere but I don't know where:
>Hapoon, the maybe head scientist that experimented on Anya, and Shopkeeper hate each other. Meaning they must know each other somehow.
>The pruners only ever seem to visit with Shopkeeper in his garden. Clients are never in the garden, but drive in plain view up to the front door. The SSS doesn't know who any of the pruners are, but the pruners also don't know they (partially) work for the SSS. This suggests that both clients and assassins are restricted to specific parts of the estate. Meaning there's potentially plenty of room to hide someone.
>The operatives aren't supposed to be around each other without express permission from Shopkeeper. The others know Yor has a family, but they don't know anything about them. Hemlock only just saw Loid for the first time. No one has seen Anya.