Based on Christoph's explanation, I can summarize as follows:
If B is a node created by a node creating macro (either \pnode or \pstGeonode) inside a transforming macro (\rput, \uput or others) then the point (!N-B.y N-B.x) provided by saveNodeCoors=true will not be the same as (!\psGetNodeCenter{B} B.y B.x) or (B). Buffering B via either \pnode(B){C} or \pstGeonode(B){C} is a way to make them behave the same.
In the following examples,
- the red dots represents dots created with
(!N-B.x N-B.y).
- the green dots represents dots created with
(!N-C.x N-C.y).
- the blue dots represents dots created with
(B) or (!\psGetNodeCenter{B} B.y B.x). As (B) behaves the same as (!\psGetNodeCenter{B} B.y B.x), only the usage of (B) is given.
The green (!N-C.x N-C.y) and blue (B) dots are placed at the same location but not for the red (!N-B.x N-B.y) dots.
Case 1: Node creation with literal (x,y)
\documentclass[pstricks,border=1cm]{standalone}
\usepackage{pst-node}
\begin{document}
\begin{pspicture}[saveNodeCoors,showgrid](4,6)
\rput(1,2){\pnode(3,4){B}}
\pnode(B){C}
\pscircle*[linecolor=red](!N-B.x N-B.y){4pt}
\pscircle*[linecolor=green](!N-C.x N-C.y){3pt}
\pscircle*[linecolor=blue](B){2pt}
\end{pspicture}
\end{document}

Remarks:
\rput(1,2){\pnode(3,4){B}}
\pnode(B){C}
produces the following result.
(B)=(1+3,2+4) <--- Effect of translation
N-B.y=4 and N-B.x=3 <--- No effect of translation
(C)=(B)=(1+3,2+4)
Case 2: Node creation with another node
\documentclass[pstricks,border=1cm]{standalone}
\usepackage{pst-node}
\begin{document}
\begin{pspicture}[saveNodeCoors,showgrid](4,6)
\pnode(3,4){A}
\rput(1,2){\pnode(A){B}}
\pnode(B){C}
\pscircle*[linecolor=red](!N-B.x N-B.y){4pt}
\pscircle*[linecolor=green](!N-C.x N-C.y){3pt}
\pscircle*[linecolor=blue](B){2pt}
\end{pspicture}
\end{document}

Remarks:
\pnode(3,4){A}
\rput(1,2){\pnode(A){B}}
\pnode(B){C}
produces the following result.
(B)=(A)=(3,4) <--- No effect of translation
N-B.y=4-2 and N-B.x=3-1 <--- Effect of translation, but it is reversed. Is it strange?
(C)=(B)=(3,4)
Recommendation
As the behavior of N-B.y and N-B.x is different from B or (!\psGetNodeCenter{B} B.y B.x), it is better to avoid using N-B.y and N-B.x. They are confusing!
\psGetNodeCenter{P}P.y P.x atan 90 sub. – Display Name Dec 14 '17 at 18:35\uput{1}[(P)]{!N-P.y N-P.x...P ist defined by\pstGeonode. All nodes defined bypst-euclare special and not saved bysaveNodeCoors. See edited answer for a fix – Dec 14 '17 at 21:35\pstGeonodebut it is about a node created inside\rput. For more details, please see my answer. – Display Name Dec 15 '17 at 18:46