A bit of an update on the sound effect.
I did a clean reinstall and that seemed to have stopped the "missing shader sound" beep from occurring in this case.
That said, now it's totally silent (or maybe really really quiet) for whatever that sound effect is supposed to be, and it is causing an AI alert which I'm guessing is not the intended behavior.
Anyway, most consistent way I've found to recreate it is using this chest in particular in The Knighton Manor: https://i.imgur.com/EPFFt6D.jpg
If you grab the Noisemaker Arrow before touching anything else in there then it should cause the seemingly missing/silent sound effect and cause an alert without triggering other sounds.
Just dropping the boot or otherwise tripping the "trap" as intended does create a bunch of audible sound effects, so I'm guessing it's just one of the sound effects getting triggered there that's affected.