I had around 6 medium lockable crates upstirs in my castle. They weren't locked down or secure. Ilogged in last night and they had decayed but the keys were laying on the floor where the crates had previously been. The bags that I placed downstairs weren't locked down or secure either. They, however, did not decay.
The fact the keys lay on the ground indicate that these did not decay. They were broken.
My guess is this likely happened from a tamed or summoned "monster". They will smash any impassable items that are not locked down. Keep in mind, energy vortexes and bladespirits can be cast onto the castle ledge, so make sure you lock down any impassable furniture/containers.