It would be preferred to be able to delete a box with samples. Not to first delete the samples in a box, and then the box.
In our case the "box" is an MTP plate. You will always take out the whole MTP plate at once. Therefore, delete a Whole plate(BOX) with samples would be best.
I agree that there should be the option to delete a whole box. There should be a warning message that you are deleting a box with samples in it, but you should be allowed to do it.