Actually, Nobu really cried because he was happy. At the end of this video:
http://www.youtube.com/watch?v=BIhbTBctPkk
Nobu was interviewed just after he got out of K&C:
And speaking of crying - here is a translated interview from before Nationals in which Nobu said that he would like to land a quad and skate a program good enough to cry afterwards:
http://www.youtube.com/watch?v=iAexoryGrFI
I don't think it's the issue of not knowing the rule/not knowing how to count... Nobunari changed his LP jump layout on the fly in every single competition he entered and his changes were CoP-smart. I think it's more the problem of handiling emotions... Many times in his interviews Nobu said in interviewsthat he has a tendency to "blank out" - to get so overwhelmed by nerves/emotions that he can barely hear his own music.
In this particular competition it looked to me as if he couldn't believe that he kanded 4-3 and went on as if it wasn't there - his jump layout was similar to that from NHK Trophy. At NHK not combo-ing the second 3A didn't hurt him, because he made up in GoEs what he lost in base value, and the 3 jump combo counted.
I found it amusing that Kurt and Tracy didn't realize he made a mistake, either - Tracy actually praised Nobu for thinking on his legs.

Takeshi Honda, on the other hand, immedialtly went "This was a fourth combination!

"