I'm pretty sure that mega potions are set to auto craft by default. Unless you're referring to the weak potions you get from the mission chest. I don't find it worthwhile to upgrade those because they don't carry over once the mission is over so you're just wasting your honey.
I'd say standard hunting time is usually anywhere between 5 to 10 minutes once you learn a monster's pattern. Sometimes less. Once you get higher damage you can hunt a lot of things in a minute or two. Some of these methods are pretty cheesy though.