It may be just a bug with the self made modpack that I've built, but I disabled both the Quiver and the Scabbard and I manage to find one of them (to be precise, a Scabbard) inside a chest. Don't know if it may also happen withthe Quiver or the Weapons (I've also disabled those as I'm okay with Vanilla weapons and the mechanics of the mod it what I was looking for), as I've not spent yet a lot of time inside the world openning loot chests.
Also, I'm not aware of how easy/difficulty could be to unregister such things from loot tables. If it's not a hard tweak, maybe an extra bool in the config to have those features appart from one another (one to disable the recipe and another to disable from loot tables).

Ill look into this.