You mean thanks the Netherlands!
John Hugenholtz designed Suzuka, along with Zandvoort, Zolder, Hockenheim and Jarama.
For the rest, totally agree with your post 
actually it was basically and practically planned and designed by a project team lead by Honda-worker Shiozaki, from start to finish. Hugenholtz's supposed to have "supervised", and did give some advice, but it's said that most of his opinion hadnt been adopted. His role and involvement was merely nominal throughout.
Also, Sohichiro Honda requested strongly that the circuit to be designed and built by not touching/changing original environment there (especially farmland) as much as possible, making the most out of natural terrain of available lands while setting preserving it as highest priority.
very 1st original plan for Suzuka circuit

for this layout, many farmlands had to be demolished so that Mr Honda rejected it.
It wasnt easy task at all for Shiozaki and co. his team had to overcome many obstacles and go through revision after revision before reaching final plan and starting construction.
revision history of layout proposal

Also, Fujisawa, then executive at Honda and Mr Honda's important partner, even mortgaged his own house in order to drive forward this project, which, at that time, was very difficult to be promoted and materialized.
That's how they'd worked on the project.
That's why the circuit looks like it threads through hills and mountains and ponds and forests. (Its rich elevation change is of natural terrain, audience stands along the track are of original hill/mountain. And there are several ponds in and around the circuit. One of the ponds in paddock area unfortunately had to be buried due to need for more space when they refurbished the circuit in 2009. Those ponds are/have been important for farming for long time. Also there's a small pond inside hairpin-backstraight triangle).
pics quoted from here
http://allabout.co.jp/gm/gc/390456/2/