Hi HK, welcome aboard.
To state things fairly, I am not a member fo the Bujinkan, Toshindo or other large Ninjutsu organisation, hwever I am a member of the original schools here in Melbourne, under the first Australian to teach the art (Bujinkan back in the day). I personally have a great deal of respect for Sensei Hayes, and feel he is owed a huge debt of gratitude for all the work he has done and all he has achieved in spreading the art worldwide. That said...
There have been numerous accounts of Hayes' plaque being taken down, first-hand accounts by students in Japan at the time, mention on many boards, including the Bujinkans' own, and, to date, no actual denial by any member involved. If you read through the interview with Sensei Hayes carefully, you may notice that the tenses used are all past when talking about Hatsumi Sensei and his training under him. The reason given for the removal of the plaque, as I understand it, is nothing to do with lack of knowledge, training, background, understanding, skill etc, but more to do with the movement away from the current Bujinkan training. You may notice that this is something that Hayes himself talks about (refering to the "ninjutsu training in the 70's" as opposed to the "Budo Taijutsu of today").
So the interview you refered to is actually very cleverly worded to give a link back to Hatsumi still, but doesn't deny the removal of the plaque (instead simply saying that Hayes has yet to hear from Hatsumi if he is out of the family, so to speak), and in all other regards actually supports everything I stated (save earlier students... but that is very well documented as well. Hayes was not the earliest American student, he was the earliest American certified teacher. Small difference).
The thing to remember when reading anything is the agenda behind it, whether from Hayes or Hatsumi, or anyone else, including myself and others here. But, as stated, I have no vested interest in Toshindo or the Bujinkan, so my agenda is just clear information. Take from it what you will.