Hi RoninX,
I want to address this post first, then we'll get to your question.
But isn´t it like teaching something that doesn´t have nothing to do with the Bujinkan? Isn´t it like teaching karaté in a Budô Taijutsu class? Shouldn´t the Shidoshi´s follow the spirit that the nº1 man in the org brings to each class? Isn´t that also part of the Bujinkan? Shouldn´t be Hatsumi making the rules? How can i, inside of an org force someone to do something that the founder of the org doesn´t care about? Once representing an org that isn´t mine, shouldn´t i do what the Boss wants, instead of what i want? And if you´re charging money to teach "Bujinkan", shouldn´t you reproduce what the Bujinkan really is, instead of creating your own Bujinkan with your own rules?
No, it's nothing like teaching karate in a Budo Taijutsu class. Part of the ranking of Shidoshi in the Bujinkan is that you are recognised as having enough of an understanding of the principles of the art to be able to pass it on accurately. Whether or not a jacket is worn is kinda unrelated to that. Bujinkan Shidoshi teach the Bujinkan arts, whether they are wearing a jacket or not. But within the Bujinkan they are given a greater-than-most degree of freedom as to how they do that for their students.
Part of the concept (and here is where we get Japanese for a moment) is that those that are not truly following what the Bujinkan teaches, and are not passing it on, will basically fade away themselves, and their students will either go to someone who does understand, or not. But in true Japanese Classical art fashion, the only person who needs to apply any standards/rules when it comes to the Bujinkan is Hatsumi, and possibly his successor. These arts are held in one individual at a time, everyone else is basically along for the ride. But in a very Japanese way, to point out the Shidoshi's mistakes/shortcomings can essentially bring about a "loss of face" for the Shidoshi, by extension their students, and their teachers. So to prevent that happening, it is left alone. That really cannot be taken as approval, or permission, though.
Now, as to how we interpret Hatsumi and the Shihan not wearing jackets, I really don't think there's much to interpret. If anything, I would look to the fact that Hatsumi Sensei tends to revel in his non-ordinary ways, and teaching classical arts in such an informal way is just one aspect of that. The other possible interpretation is that it doesn't matter whether you are wearing a jacket/gi or not, your skills should be there no matter what you are wearing at the time. But I don't pretend to speak for him, and the fact is that without asking him yourself, there is no way to know why he teaches without an uwagi. He could just get hot.