Not having the decks in the deckbox could call for other problems. First and foremost, you have four bulky items in your hands (you're usually alone when carrying the decks), which can easily evolve into a single item - on the floor.

You DO want to have the sideboard and deckbox, in case you need some extra checks, and to avoid giving the players the impression that anything fishy going in the sb is fair game because nobody checks.

The method is undoubtedly easy to understand. Unfortunately we're only human, so we are able to mess up even the simplest task. As I mentioned, this isn't a made up scenario, this is exactly what happened. It is probably the worst case scenario for this technique, but a single card could easily slip into or out of the deck. There's of course a possibility to screw up in every deck check technique, so a possible answer to this issue is “whatever”. If the eventuality is low enough, we may just neglect it.

The whole thing is: the responsibility is now on the judge, rather than the player. Are we all aware of this? Are we ok with that? Is it a good tradeoff? Can we find a way to improve this situation? Do we want to improve this situation?

I like the “whatever” camp, but maybe someone has some good idea :)
-Will