I'm wondering if there's a good way to understand damage/decay done to any building material.

I have a weird issue where one player's entire base seemed to have disappeared. It doesn't seem to have been raided but they swear they had items in their cabinet. Obviously, I don't know what to think, but was wondering if there's a good way to track this stuff with a plugin or in some other way.

Any advice is appreciated. Thanks.

The OnEntityTakeDamage hook.  Check for building parts and check the DamageType.  If it's decay or explosive, maybe add it to a log.