I don't see any reason why witchcrafting would be bad for crafting. It changes (reduces?) their chance to make magical unlock scrolls? I have no idea if or why that would be the case, but I doubt it. And even if it did, it's not like there's very many things that are hard to unlock. 98% of things can be bashed or have keys lying around somewhere nearby. For that reason, lockpicking is basically useless too. I can think one one chest I couldn't bash and could open with 4 or 5 lockpicking (I think I found it in a dirt pile). Too bad I got crap out of it.
Here's a hint about how to use magical unlock.
Use the one magic unlock scroll you are guaranteed to find in Arhu's chamber (I believe) to unlock the Chest of the Source King. It cannot be bashed or lockpicked. You find a key for it much later, but by that time the loot in the chest is probably useless for your level.