Since the game items are entirely destructible, what’s stopping someone from picking a lock or smashing a door and stealing everything I’ve spent all day crafting?
There's a few things to think about when discussing 'stealing' in Chronicles of Elyria.
A thief can only steal as much as he can carry, so it's unlikely he could rob the entire store without the use of a wagon, crate, etc. of some sorts. A guy running around with a wagon or cart will most likely be a very easy target to hunt down by law enforcement.
Time & Skill. Not only will it take the thief to picklock the door, but it will take a lot of time moving store items into their satchel or whatever they are using. One does not simply loot a store in a handful of seconds. And how long will it take for someone walking down the street to notice this? More so, this is all implying that a thief has the skill to picklock your door, maintain stealth mode, etc. Think of the paper trail as well, of a thief trying to sell stolen goods to nearby villages.
Don't worry too much about a thief 'breaking' a window or door. That's not a very stealthy way to rob a store, wouldn't you say? That would let pretty much everyone nearby know that something wrong is going on.
If you are a candlemaker, or a producer of a simple commodity, it's not the end of the world if a thief gets into your store and steals a dozen candles. Think of the hundreds of candles the store produces every week! It's akin to a thief stealing a couple of apples from a barrel.
However, if you are a jeweler, that is a different matter. If you are crafting jewels, you're dealing with a high value commodity. Therefore, you should have the means to pay for the best of locksmiths, potentially even a nighttime guard, and hopefully, you'll have everything locked in chests come night. Risk vs reward in this case :)
Part of the thrill in Elyria is creating something, protecting it, and potentially selling it sucessfully. If the world was perfectly safe, and everything you created had zero risk of being destroyed or stolen, then most things would lose a significant amount of gratifying value.
If you want to craft peacefully, then find a city that invests in their walls, law enforcement, and order. As a jeweler, I would definitely not want to be in some little village with no enforcement or defenses! I would want to be in an urban area with guards patrolling the streets.
Hope this answered part of your concerns! :)