Hey, i'm having the same issue. While it could be interesting for some people to leave full chests behind, when you use active logistic systems, it makes no sense to leave it behind as it should be empty or almost empty anyway.
EDIT: With some people of factorio discord, we found that in the control.lua file, those functions cannot work because the chests are called "logistic-something-something-1" and the functions are calling ""logistic-something-something", which is not the same.
After changing it, the chests are now vanishing when you deconstruct the mining drill, however its content is also destroyed, which means, you shouldn't deconstruct it while not empty.
Also, planning deconstruction will not work, and I don't know why
