I never really saw a connection between Dead Hand and Bongo Bongo... When I was younger, I always considered Dead Hand to be an element of the well's dark mysterious theme. You know, just a run of the mill zombie.
I have a few ideas why dungeons might be as ironic as they are.
1) Like other members have stated, the "weapons" are usually tools for whoever worshipped or worked in the temple would use to get around. It could be a coincidence that they can be used in the boss room or on the boss itself