Suggestion: Make physically bashing destroy some of the "soft items" in the crates and boxes, but not any of the harder, sturdier ones like weapons, armor and similar. Because it makes sense.
That and making bashing attract guards, raise alarms and similar (where it should be logically expected only) will provide good balance versus stealth thievery. You already have doors that cannot be physically broken, so why not a few of special crates of that kind too?
Make burning, freezing or electrocuting loot boxes destroy more items, including sturdier ones.
Also, i think if you make it that once i select attack on an item the animation of hitting it becomes automatic and repeats until it or my weapons break - so i dont have to select attack fifty times myself - will remove majority of the complaints about it.
If it was me, i would make durability have tiered negative effect on the item stats. So a player with low repair stat could only fix them partially. (same thing for loot from enemies, which will make high repair skill more valuable but players could still play without it)
I would then also use that mechanic to make items in loot boxes slightly or more damaged caused by physically or magically forcing them open.
That would also make thievery even more valuable and i think some xp for success wouldn't be amiss either.
I would also like to see lockpicks break only occasionally, due to low skills and critical fails - not all the time. So a skilled thief would not break her lockpicks all the time even if she fails to open the lock immediately. That would then become a natural sign that a lock is too difficult for that level of skill - if attempted by a skilled thief, but nothing more. The point is, skilled thieves do not break their lockpicks. And they usually dont jam the locks either.
Low skilled thieves would then break the lockpicks all the time and jam the locks all the time. Necessitating a more robust approach and loss of some items depending on whether physical or magical force is used.
If a character doesnt have any thievery skills i would completely disable the option to even attempt lockpicking.
