All four have the same meaning. Asking in the negative allows the responder to reassure the person who asked.

They can be used interchangeably, however there is a slight difference: Using "have" means the speaker is asking about a point in time in the past--the end of the packing process ("has the end been reached"). Using "are" makes the speaker sound like he is asking about the packing process--a continual action until it is done. ("Has the formerly-ongoing process been completed?")