I don't really get the question so I hope this is what you wanted. If you include a full document (such that we copy paste and see the problem on our systems) things are much more easier.
Here, you can change the default setting within a scope but your block
style had a node distance
which was resetting every time it is issued. I've made it 2mm such that we can see the difference easier.
\documentclass[tikz]{standalone}
\usetikzlibrary{arrows,shapes.geometric,positioning}
\begin{document}
\begin{tikzpicture}[decision/.style={diamond, draw, text width=4.5em, text badly centered, node distance=3.5cm, inner sep=0pt},
block/.style ={rectangle, draw, text width=6em, text centered, rounded corners, minimum height=4em, minimum height=2em},
cloud/.style ={draw, ellipse, minimum height=2em},
line/.style ={draw,-latex'},
node distance = 1cm,
auto]
\node [block] (1st) {1st};
\node [block, right= of 1st] (2nd1) {2nd1};
\begin{scope}[node distance=2mm and 10mm]%Here we change it for everything inside this scope
\node [block, above= of 2nd1] (2nd2) {2nd2};
\node [block, below= of 2nd1] (2nd3) {2nd3};
\node [block, right= of 2nd1] (3rd1) {3rd1};
\node [block, above= of 3rd1] (3rd2) {3rd2};
\node [block, above= of 3rd2] (3rd3) {3rd3};
\end{scope}
\node [block, below= of 3rd1] (3rd4) {3rd4};
\node [block, below= of 3rd4] (3rd5) {3rd5};
\path [line] (1st) -- (2nd1);
\path [line] (2nd1) -- (2nd2);
\path [line] (2nd1) -- (2nd3);
\path [line] (2nd2) -- (3rd3);
\path [line] (2nd1) -- (3rd1);
\path [line] (1st) -- (2nd1);
\end{tikzpicture}
\end{document}

The construct \vphantom
is not a math operator, thus the rules for an ordinary math atom applies for the superscript. \mathop
helps:
\documentclass{article}
\begin{document}
\[
\int^S = \mathop{\vphantom{\int}}\nolimits^S
\]
\[
\int\limits^S = \mathop{\vphantom{\int}}^S
\]
\end{document}

With package amsmath
an "empty" math operator can be declared with \DeclareMathOperator
:
\documentclass{article}
\usepackage{amsmath}
\DeclareMathOperator*{\vint}{\vphantom{\int}}
\begin{document}
\[
\int^S = \vint\nolimits^S
\]
\[
\int\limits^S = \vint^S
\]
\end{document}
In case of a larger closing delimiter, \mathclose
can help, e.g.:
\documentclass{article}
\begin{document}
\[
\Biggr)^S = \mathclose{\vphantom{\Biggr)}}^S
\]
\end{document}

I do not know, the reason for the question. If only a lonely higher superscript is needed, then an invisible \rule
or \raisebox
will help:
\documentclass{article}
\begin{document}
\[
{}^S < \rule{0pt}{2.5ex}^S < \raisebox{3ex}{$\scriptstyle S$}
\]
\end{document}

Best Answer
You can do that very simply with
\accentset
from theaccents
package. Note it is by default inscriptscriptstyle
. You can forcescriptstyle
, but the documentation of the package warns you can have trouble. In the present example, it seems to work: