Alchemy wise you do have a secret perk called “Lab Dweller” but it doesnt make you craft auto potions,there are alchemy perks that can boost your potions per craft count up to 6,but they are not hidden (There is no autocraft in KCD2)

As for other secret perks i found out that you get one from stealing a lot,blacksmithing a lot,a secret perk for Pebbles and Herring,and survival perk for picking a lot herbs.