Your post was all there was to base an answer on? If you dont like the answers that is fine, but the premise of your question is flawed. Boxes are checked in and
are loaded onto aircraft as baggage provided they satisfy all of the security and loading requirements.
Perhaps your friend could shed more light on the reasons this bag was pulled. You have already been given a number of
prima facie reasons why it might well have caused an alert. You drew attention to the fact that the box was being carried by your friend, and you drew attention to the fact that it had been couriered to a London hotel. Presumably you felt it was relevant to the issue?
When your friend was "quizzed" about the box, did his answers match the answers he gave when he checked-in? In itself, provided the box was checked and labelled, it would have been in the ordinary course of events treated as any other piece of luggage. The fact that is wasn't would suggest something was amiss. Your posting raises a number of flags, which you chose to mention, but feel are irrelevant to the answers received.
I doubt anybody is going to be able to give you a definitive answer, and most of the obvious bases have been covered.
Do the bad guys only pack their tools of mischief in cardboard boxes - ones that cannot be penetrated by security scans?
Many of us receive refresher courses in aviation security on an annual basis, and are amazed at what the "bad guys" try. In fact is often amazing at what quite ordinary people try. There have been a lot of attempted (and a few successful,) security breaches. Some of the more serious ones have been targetted at the UK and involving airlines originating at UK airports. Many of the delivery methods involve seemingly quite inoccuous packaging or contents.
Yes, there a whole raft of regulations in place that are extremely inconvenient. Whether you or I find them acceptable or understandable is irrelevant to their validity. They are either complied with, or you risk falling foul of the system in place. The result being denied carriage or the sort of inconvenience you have highlighted.
I will accept that the fragility of a box might require some different attention, but elsewhere this is taken care of by signing a form that absolves the airline of responsibility. NOT having to check it in elsewhere.
No that isn't the case (excuse the pun!) Any fragile item of baggage will often require special handling. Not just fragile items, but any other items that require special handling, just as sports equipment, outsize or heavy luggage and even ordinary crew baggage. In my job as an airline pilot I travel all over the world, both as operating crew and as a passenger. These procedures are common everywhere.