Dr. Okrand told me that the intended meaning of So' is that the subject hides the object, and that the TKD example nuqDaq So'taH yaS means "Where is the officer hiding [something]?" He apparently messed it up when he simplified the example to focus on the usage of nuqDaq. The way it's done in Star Trek Into Darkness, DaH pIghvamDaq So''eghtaH, is correct for when someone hides themselves. A So'wI' is a device that hides something else, and yISo'rup means "prepare to hide [the ship]". (This affects a line in the paq'batlh where -'egh will be added in the 2ed.)

I think he's a bit reluctant to declare that something in TKD is an error when it can be avoided, so I think what we can say about it is that So' usually means the subject hides the object (or hides something in general, if there's no object), but that for reasons unknown, there are rare instances where it's used without an object to mean the subject is hiding itself. (And then we can just ignore the TKD example sentence, since every other example uses the "subject hides object" meaning.)