In Belgium publishers are obligated to send a single copy to the national library, so in that case the only public funding that is wasted is the extra storage space, which would be rather minimal. I don't know if Japan has similar rules, but I wouldn't call it a "massive" waste compared to some other places where public money is spent.

I studied some courses on archival, so I am probably biased. I think preservation is important, and even in this case I would prefer for them to be archived too, as the box and box art are also part of the piece and of cultural significance.