I don’t know if it’s cause or effect, but there’s a lot of passing biscuits round the office everywhere I’ve worked in Japan and that usually includes leaving them on the desk for people who are elsewhere. If they aren’t individually wrapped that means walking round with a stack of paper napkins and leaving the biscuits on top of them. The few times when Japanese people have visitors in the house they tend to give snacks still in their packaging as well.
The Japanese equivalents like manju have to be individually wrapped because otherwise they all stick together, so there might be an influence of that as well. The Japanese are also far less likely to sit down and scoff a whole packet of biscuits than certain Westerners (e.g. me).
Then there is packaging still being seen as good service in Japan and the general lack of awareness of green issues…