It is a good question, I think. If Koishi is in an empty box, and you can see that there's nothing else in the box – will you really just brush it off that the totally empty box is somehow heavier if Koishi just sits there? 🤔 Or will you eventually notice the pebble?
If it's the latter, then we may simply brush Koishi's passive status effect to be natural camouflage. You will eventually see her if you've registered enough observation cues. And it also means she's practically impossible to detect in practice if she happens to be deliberately sneaky.