Well, I'm just a white belt, and unfortunately I have had to put my training on hold for short time, due to not having a job. But if you would permit me, I would like to give my take on the matter.
From the things I've read and heard, it kind of seems a mute point. Anshu Hayes has said on video that he does still offer those types of training,( herbal gathering, etc.....), to those that are interested. So I would say yes it is ninjutsu. Just not in the classical sense. Even he says, that he saw the bujinkan going in a direction he didn't care for. Putting more of a focus on the self-defense applications, than the more exotic ninjutsu teachings, and that he resisted for some time. Because he had studied ninjutsu to learn those types of things that you can't learn from other martial arts. However, he also says that he began to see the value in what Hatsumi Sensei was doing. That while there are still people that will spend the time to learn making there own gun powder, and finding herbs, etc... there is a large group that will not. They would rather concentrate on the self-defense applications.
So as a teacher, if someone comes to you and says, "Look I like what your doing self-defense wise, but I really don't have the time for some of the other things, will you teach me to protect myself?" as a teacher do you tunr that person away, because they don't or won't spend the time to learn the other aspects? Perhaps after some time in training they will, or perhaps because they have come to you and asked you to help them learn how to defend themselves you help them.
In my life time I have never met a teacher that withheld knowledge just for the sake of witholding knowledge. I think that most teachers regardless of what they teach are probably more perceptive of there students than we give them credit for. If a student is ready and willing to learn something, or has even asked I think most instructors are more than willing if they feel that person is ready, to teach it to them.
Is to-shindo still ninjutsu? In my opinion yes. I think that it is structured differently to allow a larger diversity of people to experience,( even if it just a small piece), a piece of ninjutsu. To learn a little bit about a culture, while being more susceptible for most americans to accept the teachings. This is not a bad thing. The more people that can taste something, more popular that thing becomes. The same with anything. So....people will argue probably for a long time about things that really in the grand scheme of things don't matter. What does matter is are you happy with what your being taught? Do you find value in it? Is your instructor capable of passing on to you what he has been taught? The answer for me on all levels is yes. The question for each one of is the same, and if it is yes, why bother with the other crap?
even the closest quest centers to me are across the boarder (Im learning in Canada) so any trip at all is a huge expense and Im in universcity so I dont have much disposable income 
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