1 - I had boots go "invisible" in the inventory, i.e. their icon was not displayed. But as I had just used "arrange by type" and the junkyard

was orderly, I guessed that the empty box - amidst other "stuff" - could be the missing item.
2 - I had a problem with shovels "refusing to work" - everybody had a shovel but I got "I will not dig with my hands" replies. This issue was caused by the "named shovel" from the cave leading to the cellar under the Apothecary in Blighted Village.
But empty inventories do happen - e.g. in one playthrough Shadowheart, freshly out of the Nautiloid, on the beach, had an EMPTY inventory. No scrolls, no Magical 20 of World Salvation, no Health Potions, nothing!
A known issue, the inventory magcally refilled itself a minute and a a few clicks later :P